[gmx-users] Generate topology

[Justin Lemkul]

On 7/19/13 8:53 AM, afsaneh maleki wrote:
> Dear   Justin
>
>   I want a topology for an arbitrary molecule (44 atom) and I use x2top
> program that .n2t file is it’s input.
>
> The .pdb file is as the following:
>
> ATOM      1  O5  TPT     1      -6.131  -0.245   0.000  0.000000
>
> ATOM      2  C21 TPT     1      -5.041   0.384   0.000  0.000000
>
> ATOM      3  O6  TPT     1      -5.040   1.814   0.000  0.000000
>
> ATOM      4  H12 TPT     1      -5.945   2.134   0.000  0.000000
>
> ATOM      5  C18 TPT     1      -3.708  -0.387   0.000  0.000000
>
> ATOM      6  C19 TPT     1      -2.374   0.383   0.000  0.000000
>
> ATOM      7  H10 TPT     1      -2.373   1.453   0.000  0.000000
>
> ……
>
> I copied oplsaa.ff folder in my working directory
>
> atomname2type.n2t file is as the following:
>
> O  opls_267   -0.495284   15.9994   1 C 0.1214
>
> C  opls_470    0.594326   12.0110   3 C 0.1487  O  0.1306   O  0.1214
>
> O  opls_268   -0.560735   15.9994   2 C 0.1306  H  0.0974
>
> H  opls_270    0.417334    1.0079   1 O 0.0974
>
> C  opls_145    0.037549   12.0110   3 C 0.1487  C 0.1387  C 0.1387
>
> C  opls_145   -0.145422   12.0110   3 C 0.1387  H 0.1087 C 0.1395
>
> H  opls_146    0.110842    1.0079   1 C 0.1087
>
> ……
>
> I used   these command:
>
> ] g_x2top  –f  .pdb  –o .top  -pbc –ff oplsaa
>
>
>
> But I get:
>
> opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t
>
> There are 23 name to type translations in file oplsaa.ff
>
> Generating bonds from distances...
>
> atom 44
>
> Can not find forcefield for atom C21-2 with 3 bonds
>
> Can not find forcefield for atom C18-5 with 3 bonds
>
> Can not find forcefield for atom C16-10 with 3 bonds
>
> Can not find forcefield for atom C20-11 with 3 bonds
>
> Can not find forcefield for atom C15-17 with 3 bonds
>
> Can not find forcefield for atom C12-18 with 3 bonds
>
> Can not find forcefield for atom C7-27 with 3 bonds
>
> Can not find forcefield for atom C5-28 with 3 bonds
>
> Can not find forcefield for atom C3-33 with 3 bonds
>
> Can not find forcefield for atom C2-34 with 3 bonds
>
> Can not find forcefield for atom C9-40 with 3 bonds
>
> Can not find forcefield for atom C10-41 with 3 bonds
>
>
>
> Program g_x2top, VERSION 4.5.4
>
> Source code file: g_x2top.c, line: 206
>
>
>
> *Fatal error:*
>
> Could only find a forcefield type for 32 out of 44 atoms.
>
>
>
>
>
> How to solve my problem.
>
> Why do gromacs open /
> usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I
> copyied oplsaa.ff
> folder in my working directory. Also I edited  .n2t file in my folder.
>

Put the .n2t file in the working directory, not in an oplsaa.ff subdirectory.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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