[gmx-users] how to use atom2cg.awk

Justin A. Lemkul jalemkul at vt.edu
Tue May 12 04:02:09 CEST 2009


I have discovered two other potential errors in the script:

1. Coordinates are not processed quite right; this leads to a molecule with the 
correct shape, but some residues are scrambled.
2. ILE residues are not handled correctly (only a backbone particle is generated)

I modified the script, and it is working in my own internal tests.  I would 
suggest using the script below.

-Justin

-------

#!/usr/bin/awk -f
#Converts Atomic PDB file to Coarse-grain PDB file
#The atom types are default values - BN0, SC1, SC2
#Should be corrected by using correct itp file
#if columns are not separate (e.g. x or y or z > 99) the script doesnt work
#in that case insert an empty column or use PDBCat to separate columns
#d! groningen   29.01.08

{if 
($1=="HEADER"||$1=="REMARK"||$1=="CRYST1"||$1=="MODEL"||$1=="TER"||$1=="ENDMDL"||$1=="END")
print $0
if($1=="ATOM" && $4=="ARG" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if($1=="ATOM" && $4=="ARG" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if($1=="ATOM" && $4=="ARG" && $3=="NE")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ALA" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASN" && $3=="CA" )
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASN" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASP" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASP" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="CYS" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="CYS" && $3=="SG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLN" && $3=="CA" )
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLN" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLU" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLU" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLY" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="ND1")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="NE2")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC3", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ILE" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ILE" && ($3=="CD" || $3=="CD1"))
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LEU" && $3=="CA" )
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LEU" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LYS" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LYS" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LYS" && $3=="CE")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="MET" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="MET" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CE1")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CE2")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC3", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PRO" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PRO" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="SER" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="SER" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="THR" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="THR" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CD1")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CD2")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CE2")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC3", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CH2")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC4", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CG")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CE1")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC2", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CE2")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC3", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="VAL" && $3=="CA")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "BN0", 
$4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="VAL" && $3=="CB")
printf("%4s  %5i %4s %3s  %4i    %8.3f%8.3f%8.3f%6.2f%6.2f    \n",$1, $2, "SC1", 
$4, $5, $6, $7, $8, $9,$10,$11);
}


xi zhao wrote:
> Dear Sir:
> The script can produce correct structure,thank you very much!
> Best regards!
> Zhao xi
> 
> 
> 4 
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
> --- *09年5月11日,周一, Justin A. Lemkul /<jalemkul at vt.edu>/* 写道:
> 
> 
>     发件人: Justin A. Lemkul <jalemkul at vt.edu>
>     主题: Re: [gmx-users] how to use atom2cg.awk
>     收件人: "Gromacs Users' List" <gmx-users at gromacs.org>
>     日期: 2009年5月11日,周一,下午9:35
> 
> 
> 
>     Justin A. Lemkul wrote:
>      >
>      >
>      > xi zhao wrote:
>      >> But CG structure and native PDB structure is very different,
>     please see my attaches.
>      >>
>      >>
>      >
>      > Remove the chain identifier from the input structure.  You'll
>     note that the x-coordinate of each atom in the output is the residue
>     number, so the chain identifier is throwing off the awk field count.
>      >
>      > -Justin
>      >
>      >>
>      >> 4
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>
>      >> --- *09年5月11日,周一, Justin A. Lemkul /<jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/* 写道:
>      >>
>      >>
>      >>     发件人: Justin A. Lemkul <jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>      >>     主题: Re: [gmx-users] how to use atom2cg.awk
>      >>     收件人: "Gromacs Users' List" <gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >>     日期: 2009年5月11日,周一,下午8:33
>      >>
>      >>
>      >>
>      >>     xi zhao wrote:
>      >>      > Dear sir:
>      >>      > This is my modified script, please see it! I take CG
>     simulations     according to 
>     http://md.chem.rug.nl/marrink/coarsegrain.html.
>      >>      > Thank you !
>      >>      >
>      >>
>      >>     Then your structure should be built appropriately.
>      >>
>      >>     -Justin
>      >>
>      >>      >
>      >>      > 4
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>
> 
>      >>      >
>      >>      > --- *09年5月11日,周一, Justin A. Lemkul
>     /<jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>     写道:
>      >>      >
>      >>      >
>      >>      >     发件人: Justin A. Lemkul <jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>      >>      >     主题: Re: [gmx-users] how to use atom2cg.awk
>      >>      >     收件人: "Gromacs Users' List" <gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >>      >     日期: 2009年5月11日,周一,下午6:49
>      >>      >
>      >>      >
>      >>      >
>      >>      >     xi zhao wrote:
>      >>      >      > Dear Sir:
>      >>      >      > In fact, I have modified the script as you said,
>     but the CG
>      >>      >     strucrute produced is not different  in secondary
>     strucure with
>      >>      >     native PDB structure: CG structure became a line
>     strucrue! Please
>      >>      >     help me! Or give me a good script!
>      >>      >
>      >>      >     Visualization is not an appropriate method to use to
>      >>     determine the
>      >>      >     validity of your procedure.  The CG model will look a
>     bit strange
>      >>      >     when rendered as "lines" in most visualization
>     software.  You did
>      >>      >     modify each line of the script, inserting $5 between
>     every $4 and
>      >>      >     $6, correct?
>      >>      >
>      >>      >     -Justin
>      >>      >
>      >>      >      > Thank you very much!
>      >>      >      > Best regards!        >
>      >>      >      > 4
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>>
> 
>      >>      >      >
>      >>      >      > --- *09年5月11日,周一, Justin A. Lemkul
>     /<jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>      >>     写道:
>      >>      >      >
>      >>      >      >
>      >>      >      >     发件人: Justin A. Lemkul <jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>      > 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>      >>      >      >     主题: Re: [gmx-users] how to use atom2cg.awk
>      >>      >      >     收件人: "Gromacs Users' List"
>     <gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >>      >      >     日期: 2009年5月11日,周一,上午8:22
>      >>      >      >
>      >>      >      >
>      >>      >      >
>      >>      >      >     xi zhao wrote:
>      >>      >      >      > Dear sir :
>      >>      >      >      > how to motify the $5 in details?
>      >>      >      >      > Thank you!
>      >>      >      >      >
>      >>      >      >
>      >>      >      >     Use a text editor (vi, emacs, gedit, etc),
>     like you
>      >>     would to
>      >>      >     create
>      >>      >      >     any script.
>      >>      >      >
>      >>      >      >     -Justin
>      >>      >      >
>      >>      >      >      >
>      >>      >      >      >
>      >>      >      >      > 4
>      >>      >      >       
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>
> 
>      >>      >      >       
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>>>
> 
>      >>      >      >      >
>      >>      >      >      > --- *09年5月8日,周五, Justin A. Lemkul
>      >>     /<jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>      > 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>      >      >       
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>      >>      >     写道:
>      >>      >      >      >
>      >>      >      >      >
>      >>      >      >      >     发件人: Justin A. Lemkul
>     <jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>      > 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>      >>      >      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>      >>      >      >      >     主题: Re: [gmx-users] how to use
>     atom2cg.awk
>      >>      >      >      >     收件人: "Discussion list for GROMACS users"
>      >>      >      >     <gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >      >       
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >>      >      >      >     日期: 2009年5月8日,周五,下午6:46
>      >>      >      >      >
>      >>      >      >      >
>      >>      >      >      >
>      >>      >      >      >     xi zhao wrote:
>      >>      >      >      >      >
>      >>      >      >      >      >
>      >>      >      >      >      > Dear Sirs:
>      >>      >      >      >      >   I wang to know simulate coarse-graied
>      >>     system using
>      >>      >      >     gromacs, but
>      >>      >      >      >     I don not know how to use atom2cg.awk to
>      >>     convert CG model!
>      >>      >      >      >      > Thank you very much!
>      >>      >      >      >      >
>      >>      >      >      >
>      >>      >      >      >     ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb
>      >>      >      >      >
>      >>      >      >      >     Note that the script available online
>     needs to be
>      >>      >     modified to
>      >>      >      >      >     include a $5 between the $4 and $6 on each
>      >>     line, otherwise
>      >>      >      >     you will
>      >>      >      >      >     get an incorrectly-formatted .pdb file.
>      >>      >      >      >
>      >>      >      >      >     -Justin
>      >>      >      >      >
>      >>      >      >      >      > 4
>      >>      >      >      >             
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>
> 
>      >>      >      >       
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>>
> 
>      >>      >      >      >             
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>
> 
>      >>      >      >       
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
> 
>      >>      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
>      >> 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>>>>
> 
>      >>      >      >      >      >
>      >>      >      >      >      >
>      >>      >      >      >      >
>      >>      >      >      >             
>     ------------------------------------------------------------------------
>      >>      >      >      >      > 好玩贺卡等你发,邮箱贺卡全新上线!
>      >>      >      >      >             
>     <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
> 
>      >>      >      >      >
>      >>      >      >      >      >
>      >>      >      >      >      >
>      >>      >      >      >      >
>      >>      >      >      >             
>     ------------------------------------------------------------------------
>      >>      >      >      >      >
>      >>      >      >      >      >
>     _______________________________________________
>      >>      >      >      >      > gmx-users mailing list   
>        gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >      >       
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >      >      >             
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >      >      >      >
>      >>     http://www.gromacs.org/mailman/listinfo/gmx-users
>      >>      >      >      >      > Please search the archive at
>      >>      >     http://www.gromacs.org/search
>      >>      >      >     before
>      >>      >      >      >     posting!
>      >>      >      >      >      > Please don't post (un)subscribe
>     requests to the
>      >>      >     list. Use
>      >>      >      >     the www
>      >>      >      >      >     interface or send it to
>      >>     gmx-users-request at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
> 
>      >>      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
> 
>      >>      >      >       
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
> 
>      >>      >      >      >             
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
> 
>      >>      >      >      >      > Can't post? Read
>      >>      >      >     http://www.gromacs.org/mailing_lists/users.php
>      >>      >      >      >
>      >>      >      >      >     -- ========================================
>      >>      >      >      >
>      >>      >      >      >     Justin A. Lemkul
>      >>      >      >      >     Ph.D. Candidate
>      >>      >      >      >     ICTAS Doctoral Scholar
>      >>      >      >      >     Department of Biochemistry
>      >>      >      >      >     Virginia Tech
>      >>      >      >      >     Blacksburg, VA
>      >>      >      >      >     jalemkul[at]vt.edu | (540) 231-9080
>      >>      >      >      >       
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >>      >      >      >
>      >>      >      >      >     ========================================
>      >>      >      >      > 
>        _______________________________________________
>      >>      >      >      >     gmx-users mailing list   
>     gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >      >       
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >      >      >             
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >>      >      >      > 
>        http://www.gromacs.org/mailman/listinfo/gmx-users
>      >>      >      >      >     Please search the archive at
>      >>      >     http://www.gromacs.org/search before
>      >>      >      >      >     posting!
>      >>      >      >      >     Please don't post (un)subscribe
>     requests to the
>      >>     list.
>      >>      >     Use the
>      >>      >      >      >     www interface or send it to
>      >>      >     gmx-users-request at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
>      >> 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
> 
>      >>      >       
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
> 
>      >>      >      >       
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
> 
>      >>      >      >      >             
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
> 
>      >>      >      >      >     Can't post? Read
>      >>      >     http://www.gromacs.org/mailing_lists/users.php
>      >>      >      >      >
>      >>      >      >      >
>      >>      >      >      >
>      >>      >      >       
>        ------------------------------------------------------------------------
>      >>      >      >      > 好玩贺卡等你发,邮箱贺卡全新上线!
>      >>      >      >       
>        <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
> 
>      >>      >      >
>      >>      >      >
>      >>      >      >     -- ========================================
>      >>      >      >
>      >>      >      >     Justin A. Lemkul
>      >>      >      >     Ph.D. Candidate
>      >>      >      >     ICTAS Doctoral Scholar
>      >>      >      >     Department of Biochemistry
>      >>      >      >     Virginia Tech
>      >>      >      >     Blacksburg, VA
>      >>      >      >     jalemkul[at]vt.edu | (540) 231-9080
>      >>      >      > 
>        http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >>      >      >
>      >>      >      >     ========================================
>      >>      >      >     _______________________________________________
>      >>      >      >     gmx-users mailing list   
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>     ------------------------------------------------------------------------
>      >>      >      > 好玩贺卡等你发,邮箱贺卡全新上线!
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>      >>      >
>      >>      >
>      >>      >     -- ========================================
>      >>      >
>      >>      >     Justin A. Lemkul
>      >>      >     Ph.D. Candidate
>      >>      >     ICTAS Doctoral Scholar
>      >>      >     Department of Biochemistry
>      >>      >     Virginia Tech
>      >>      >     Blacksburg, VA
>      >>      >     jalemkul[at]vt.edu | (540) 231-9080
>      >>      >     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >>      >
>      >>      >     ========================================
>      >>      >     _______________________________________________
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>        ------------------------------------------------------------------------
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>      >> 
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> 
>      >>
>      >>      >
>      >>
>      >>     -- ========================================
>      >>
>      >>     Justin A. Lemkul
>      >>     Ph.D. Candidate
>      >>     ICTAS Doctoral Scholar
>      >>     Department of Biochemistry
>      >>     Virginia Tech
>      >>     Blacksburg, VA
>      >>     jalemkul[at]vt.edu | (540) 231-9080
>      >>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >>
>      >>     ========================================
>      >>     _______________________________________________
>      >>     gmx-users mailing list    gmx-users at gromacs.org
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>     <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
> 
>      >
> 
>     -- ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     _______________________________________________
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>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> ------------------------------------------------------------------------
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> <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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