[gmx-users] x2top, error generating topology

[David van der Spoel]

Vitaly Chaban wrote:
> Hello All,
> 
> I've got a problem with x2top in gromacs 3.3.3. Trying to obtain
> atopology from ".pdb" structure I do the following:
> 1. Add
>>> C C 1 C ; CNT Carbon with one bond
>>> C C 2 C C ; CNT double bonded Carbon
> to ffencadv.n2t.
> 
> 2. Add the following lines
> [ bondtypes ]
> ; i j func b0 kb
> C C 1 0.14210 478900.
> 
> [ angletypes ]
> ; i j k func th0 cth
> C C C 1 120.000 397.480
> 
> [ dihedraltypes ]
> ; i l func q0 cq
> C C 1 0.000 167.360
> 
> to ffgmxbon.itp.

that should be ffencadvbon.itp I presume?

> 
> 3. Then I execute: x2top -f cnt.pdb -o cnt.top
> where cnt.pdb is from http://turin.nss.udel.edu/research/tubegenonline.html
> 
> During the processing I select
> 7: Encad all-atom force field, using scaled-down vacuum charges
> 
> The output is
> Looking whether force field files exist
> Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp
> Opening library file ffencadv.n2t
> WARNING: all CONECT records are ignored
> Opening library file ffencadv.n2t
> There are 0 name to type translations
> Generating bonds from distances...
> atom 144
> Can not find forcefield for atom C-1 with 0 bonds
> Can not find forcefield for atom C-2 with 0 bonds
> Can not find forcefield for atom C-3 with 0 bonds
> Can not find forcefield for atom C-4 with 0 bonds
> Can not find forcefield for atom C-5 with 0 bonds
> Can not find forcefield for atom C-6 with 0 bonds
> Can not find forcefield for atom C-7 with 0 bonds
> Can not find forcefield for atom C-8 with 0 bonds
> Can not find forcefield for atom C-9 with 0 bonds
> Can not find forcefield for atom C-10 with 0 bonds
> ............................
> ............................
> -------------------------------------------------------
> Program x2top, VERSION 3.3.3
> Source code file: x2top.c, line: 206
> 
> Fatal error:
> Could only find a forcefield type for 0 out of 144 atoms
> 
> I had not got this error when using  version 3.3.1 with this
> particular task. Why does it consider the carbon has zero bonds...?
> 
> Any ideas what to do would be gratefully appreciated.
> 
> Vitaly
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se