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

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 6 20:58:54 CEST 2009 

darrellk at ece.ubc.ca wrote:
> 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
> below?
> 
> 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.
Encad is not made for vacuum. You have to verify your force field 
anyway, for publication purposes. OPLS will work just fine though.


>>
>> 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.
Check archive of the mailing list. This tool will be replaced in the 
near future (5.0), therefore there is no documentation.


>>
>> Thanks again in advance.
>>
>> Darrell
>>
>>>> -------------------------------------------------------
>>>> 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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-- 
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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