[gmx-users] Generate topology

[afsaneh maleki]

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.




Thanks in advance,
Afsaneh