[gmx-users] Topology file-residue unknown

[Justin Lemkul]

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

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