[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
> 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://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>.
>
> >> > > 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 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://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>
>
> >> >
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>
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> >>
> ------------------------------------------------------------------------
> >> > 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
> >>
> >> ========================================
> >> _______________________________________________
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> >>
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> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
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> >>
> ------------------------------------------------------------------------
> >> 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 gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
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> <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
>
>
> ------------------------------------------------------------------------
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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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