[gmx-users] Generate topology -2

[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 edited 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



And gromacs get me:



opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 names 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 for more
information and tips for troubleshooting,

…………………………………………………..



I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as the above mentioned in my working
directory.



How to solve my problem?

Why do gromacs open /
usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t?



 Thanks in advance,

Afsaneh