darre...@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, "<darre...@localhost>" <> wrote:
Date: Wed, 01 Apr 2009 22:38:28 +0200
From: David van der Spoel <sp...@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@gromacs.org>
Message-ID: <49d3d0c4.4040...@xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
darre...@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
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
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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
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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