[gmx-users] x2top & Encad all-atom force field (vacuum)

darrellk at ece.ubc.ca darrellk at ece.ubc.ca
Mon Apr 6 19:18:37 CEST 2009

Dear All,
I am resubmitting my question below as I did not receive a response and
am thinking that my previous e-mail was not recognized by the system or
missed. Could someone please provide me with an answer to my questions

Many thanks.

Darrell Koskinen

On 4/2/2009, "<darrellk at localhost>" <> wrote:

>>Date: Wed, 01 Apr 2009 22:38:28 +0200
>>From: David van der Spoel <spoel at xray.bmc.uu.se>
>>Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum)
>>	not	recognizing bonds
>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>Message-ID: <49D3D0C4.4040206 at xray.bmc.uu.se>
>>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>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.
>My gro file does contain H atoms as well. In my extract of the gro file I
>only showed the first few lines of the gro file and these lines only
>have C atoms. Note that I receive the same message for the C atoms (i.e.
>"Can not find forcefield for atom C-1 with 0 bonds").
>I actually created the files ffencadv.n2t & ffgmx.n2t in my working
>directory since the only n2t file I could find in the gromacs directory
>was the ffoplsaa.n2t file and the tutorial did not mention the
>ffoplsaa.n2t file. Should I be modifying the ffoplsaa.n2t file instead?
>If so, can you please provide me some direction on what needs to be
>added to this file so that it recognizes the atoms in my graphene
>structure as I looked at this file but do not understand what some of
>the columns represent.
>Also, I thought that ffoplsaa was to be used for liquids and since my
>simulation is in an air environment, I thought that I should be using
>the encad force field in a vacuum and should therefore be modifying an
>encad n2t file. Please correct me if I am wrong.
>Also, could you also please explain the purpose of the n2t file as I
>looked in the gromacs manual and see no description of files with the
>n2t extension and their purpose.
>Thanks again in advance.
>>> -------------------------------------------------------
>>> 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 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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