[gmx-users] Topology file-residue unknown

Juliette N. joojoojooon at gmail.com
Fri Apr 5 00:17:22 CEST 2013


Hi Justin,

Thanks a lot for your message. I am petrified why pdb2gmx is not
recognizing the residue ETY. This the first residue added to ffoplsaa.rtp
but as you may see below it is not read from rtp.

I am sure this residue is added to ffoplsaa.rtp which is existing in the
working directory:

[ ETY ]
 [ atoms ]
   C1    opls_143    -0.120    1
   H11   opls_144     0.060    1
   H12   opls_144     0.060    1
   C2    opls_143    -0.120    2
   H21   opls_144     0.060    2
   H22   opls_144     0.060    2

[ bonds ]
   C1    H11
   C1    H12
   C1    C2
   C2    H21
   C2    H22
  ;C2    C1

Then I issue:

pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa
                         :-)  G  R  O  M  A  C  S  (-:

                      GROwing Monsters And Cloning Shrimps

                            :-)  VERSION 4.5.4  (-:

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat

Select the Water Model:
 1: TIP4P  TIP 4-point, recommended
 2: TIP3P  TIP 3-point
 3: TIP5P  TIP 5-point
 4: SPC    simple point charge
 5: SPC/E  extended simple point charge
 6: None
6
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading Ethylene.gro...
Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 1 residues with 6 atoms

  chain  #res #atoms
  1 ' '     1      6

No occupancies in Ethylene.gro
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 56
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb

Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1#
Processing chain 1 (6 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: resall.c, line: 581

Fatal error:
Residue 'ETY' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am kind of baffled what could be wrong. I would really appreciate if you
could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I
doubt)?
Do i have to edit esiduetypes.dat?

Thank you many times for your precious time,




On 4 April 2013 17:21, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/4/13 11:38 AM, Juliette N. wrote:
>
>> Dear all,
>>
>> I am having trouble creating topology file for simple molecule ethylene.
>> Here is the steps. Below is the pdb file:
>>
>> Ethylene.pdb:
>>
>>
>> ATOM      1  C1  ETY     1      0.672  -0.000   0.000  1.00  0.00
>> C
>> ATOM      2  C2  ETY     1     -0.672  -0.000   0.000  1.00  0.00
>> C
>> ATOM      3  H11 ETY     1      1.238  -0.928   0.000  1.00  0.00
>> H
>> ATOM      4  H12 ETY     1      1.238   0.928   0.000  1.00  0.00
>> H
>> ATOM      5  H21 ETY     1     -1.238  -0.928   0.000  1.00  0.00
>> H
>> ATOM      6  H22 ETY     1     -1.238   0.928   0.000  1.00  0.00
>> H
>> END
>>
>> Then:
>> editconf -f Ethylene.pdb -o Ethylene.gro
>>
>> Ethylene.gro:
>>
>>      6
>>      1ETY     C1    1   0.067  -0.000   0.000
>>      1ETY     C2    2  -0.067  -0.000   0.000
>>      1ETY    H11    3   0.124  -0.093   0.000
>>      1ETY    H12    4   0.124   0.093   0.000
>>      1ETY    H21    5  -0.124  -0.093   0.000
>>      1ETY    H22    6  -0.124   0.093   0.000
>>     0.00000   0.00000   0.00000
>>
>>
>> Then I add the following residue for ethylene to the rtp file
>> ffoplsaa.rtp:
>>
>> [ ETY ]
>>   [ atoms ]
>>     C1    opls_143    -0.120    1
>>     H11   opls_144     0.060    1
>>     H12   opls_144     0.060    1
>>     C2    opls_143    -0.120    2
>>     H21   opls_144     0.060    2
>>     H22   opls_144     0.060    2
>>
>> [ bonds ]
>>     C1    H11
>>     C1    H12
>>     C1    C2
>>     C2    H21
>>     C2    H22
>>     C2    C1
>>
>>
> "C1 C2" and "C2 C1" are redundant.  You don't need both.
>
>
>  and then
>>
>> ; pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa
>>
>> Q1_ i dont realize what is the difference between the already created
>> Ethylene.gro and the one in the pdb2gmx(GRO.gro). I am not getting the
>> latter and was wondering what would be the diffrence?
>>
>>
> pdb2gmx produces an output coordinate file as a byproduct of its massively
> complicated fix-build-process procedure.
>
> If you're not getting the output file(s), then pdb2gmx is failing and
> should produce obvious error messages.
>
>
>  Q2) Below is the  top file which is not generated. Once I Issue pdb2gmx, I
>> enter "6" because pdb2gmx output says:
>>
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/watermo$
>>   1: TIP4P  TIP 4-point, recommended
>>   2: TIP3P  TIP 3-point
>>   3: TIP5P  TIP 5-point
>>   4: SPC    simple point charge
>>   5: SPC/E  extended simple point charge
>>   6: None
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/aminoac$
>> No occupancies in Ethylene.gro
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/atomtyp$
>>
>> And finally I get a blank top file::
>>
>> ;    File 'Ethylene.top' was generated
>> ;    By user: onbekend (0)
>> ;    On host: onbekend
>> ;    At date:
>> ;
>> ;    This is a standalone topology file
>> ;
>> ;    It was generated using program:
>> ;    pdb2gmx - VERSION 4.5.4
>> ;
>> ;    Command line was:
>> ;    pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa
>> ;
>> ;    Force field was read from the standard Gromacs share directory.
>> ;
>>
>> ; Include forcefield parameters
>> #include "oplsaa.ff/forcefield.itp"
>>
>>
>> -------------------------
>> output says:
>>
>> Select the Water Model:
>> Reading Ethylene.gro...
>> Read 'GROningen Mixture of Alchemy and Childrens' Stories', 6 atoms
>> Analyzing pdb file
>> Splitting PDB chains based on TER records or changing chain id.
>> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
>>
>>    chain  #res #atoms
>>    1 ' '     1      6
>>
>> Reading residue database... (oplsaa)
>> Processing chain 1 (6 atoms, 1 residues)
>> Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA.
>> Problem with chain definition, or missing terminal residues.
>> This chain does not appear to contain a recognized chain molecule.
>> If this is incorrect, you can edit residuetypes.dat to modify the
>> behavior.
>>
>>
> There should be more output after this line.  Any reason for pdb2gmx to
> fail would be printed here.
>
>
>
>>
>> Is there something wrong with my rtp? Could I trouble you to let me know
>> what wrong is?
>>
>>
> I can see nothing wrong.  I was able to produce a sensible topology using
> all of your input files.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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-- 
Thanks,
J. N.



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