[gmx-users] x2top & Encad all-atom force field (vacuum) not recognizing bonds

[David van der Spoel]

darrellk at ece.ubc.ca wrote:
> Dear All,
> I have been trying to determine why I am experiencing problems when I run
> a gromacs file through x2top. I have checked my gromacs file with VMD to
> ensure that the file is correct and VMD validates that my file is
> correct as I see the intended structure. Thus, the atoms are indeed
> located within reasonable distance from each other such that x2top
> should be recognizing the bonds.
> 
> Here is an extract from my gromacs file:
> 
>     2Grph C        1   0.000   0.000   0.000  0.0000  0.0000  0.0000
>     2Grph C        2   0.071  -0.123   0.000  0.0000  0.0000  0.0000
>     2Grph C        3   0.071   0.123   0.000  0.0000  0.0000  0.0000
>     2Grph C        4  -0.142   0.000   0.000  0.0000  0.0000  0.0000
>     2Grph C        5  -0.000  -0.250   0.000  0.0000  0.0000  0.0000
>     2Grph C        6   0.210  -0.120   0.000  0.0000  0.0000  0.0000
> 
> I thought that in order to make x2top work correctly that I would have to
> modify the files as described in Christopher Stiles website
> (http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the
> following files and saved them in my working directory:
> ffencadv.n2t
> ffgmx.n2t
> ffgmxbon.itp
> 
> I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in
> one post that this file should be renamed as such.
> 
> After all these changes, I still experience a problem when I run the
> command:
> x2top -ff select -f graphene_nm.gro -o graphene_nm.top
> selecting option  7: Encad all-atom force field, using scaled-down vacuum
> charges
> 
> When I run the above command, I receive output telling me that the atoms
> have 0 bonds. An extract of the output appears below for your reference.
> Can not find forcefield for atom H-266 with 0 bonds
> Can not find forcefield for atom H-267 with 0 bonds
> Can not find forcefield for atom H-268 with 0 bonds
> Can not find forcefield for atom H-269 with 0 bonds
> Can not find forcefield for atom H-270 with 0 bonds


Could there still be an error in your  gro file, as it seems to contain 
only C, and the error message points to H. x2top might work slightly 
better in 4.0.x. And by the way, this tutorial may be slightly 
confusing. The only thing you need to do is edit the .n2t file 
corresponding to your force field. I don't recall what is supplied in 
3.3, but in 4.0 it is ffoplsaa.n2t.

> 
> -------------------------------------------------------
> 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 270 atoms
> -------------------------------------------------------
> 
> Could you please help me resolve this issue?
> 
> Thank you in advance for your assistance.
> 
> Darrell Koskinen
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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