[gmx-users] building Topologies

[Justin A. Lemkul]

Jessé Nóbrega wrote:
> Hi gmx-users,
> 
> I have trying build topologies for PVC polymer in opls/aa forcefield. I 
> read the chapter 5 and modified the files ffoplsaa.rtp, ffoplsaa.hdb, 
> ffoplsaa-n.tdb, ffoplsaa-c.tdb, but not successful.
> Below, you can see the blocks that built. The parameters for the residue 
> may seem confusing, but I am trying to understand how to build these 
> blocks and then create new parameters for the residue.
> 
> rtp file:
> 
> [ VIN ]
>  [ atoms ]
>     C1    opls_136    -0.120    1
>    H11   opls_140     0.060    1
>    H12   opls_140     0.060    1
>     C2    opls_001     0.500    2
>     Cl     opls_151    -0.200    2
>    H21   opls_153     0.103    2
>  [ bonds ]
>    C1      H11
>    C1      H12
>    C1       C2
>    C2       Cl
>    C2      H21
>    C2      +C1
> 
> hdb file
> 
> VIN     2
>             2       6       H1       C1      C2     +C1
>             1       6       H2       C2      C1     -C2
> 
> -c.tdb file:
> 
> [ VIN ]
>  [ replace ]
>     C1      opls_135        12.011  -0.18
>  [ add ]
>     3        4      H1      C1      C2
>             opls_140       1.008   0.06
> [ delete ]
>    H21
> 
> -n.tdb file:
> 
> [ VIN ]
> [ replace ]
> C               opls_152        12.011 -0.006
> [ add ]
> 2      4        H       C2      C1
>        opls_153        1.00800  0..103
> [ delete ]
>   H21
> 
> By using the pdb2gmx following error occurs:
> 
> Opening library file ffoplsaa.rtp
> Opening library file /usr/local/gromacs332/share/gromacs/top/aminoacids.dat
> Reading PVC_32_mon_1_cd_gromos.pdb...
> WARNING: all CONECT records are ignored
> Read 194 atoms
> Opening library file /usr/local/gromacs332/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 32 residues with 194 atoms
> 
>   chain  #res #atoms
>   1 ' '    32    194
> 
> All occupancies are one
> Opening library file /usr/local/gromacs332/share/gromacs/top/ffoplsaa.atp
> Atomtype 817
> Reading residue database... (ffoplsaa)
> Opening library file ffoplsaa.rtp
> Residue 57
> Sorting it all out...
> Opening library file ffoplsaa.hdb
> Opening library file ffoplsaa-n.tdb
> 
> -------------------------------------------------------
> Program pdb2gmx_mpi, VERSION 3.3.2
> Source code file: h_db.c, line: 95
> 
> Fatal error:
> Error in hdb file ffoplsaa-n.tdb:
> Wrong number of control atoms (2 iso 3) on line:
> 2      4        H       C2      C1
> 
> Why this error occur?
> 

You need three control atoms; you only have two (2 iso 3 means "2 instead of 
3").  Refer to the manual for the proper syntax for these entries.

You may find this post helpful:

http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html

It refers to building a polyethylene polymer topology, but I think some of the 
information should be generally applicable.

Also, don't bother with -n.tdb and -c.tdb files.  If pdb2gmx does not detect 
protein, I think these files are ignored.  At least, it seems that way based on 
others' difficulties.

-Justin

> Excuse me my English, I am a beginner in the language.
> 
> Thank you very much
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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