[gmx-users] Problems using grompp and amber force field
Maik Goette
mgoette at mpi-bpc.mpg.de
Tue May 8 09:40:49 CEST 2007
Yes, the 3.3.1 amber-FFs should be used, because the implementation of
the QM/MM parts changed the format in some FF-parameters files.
I would suggest, not to use the OPLS-DNA parameter set, because it isn't
published, yet (as I know) and also uses RESP-charges, which may also be
problematic with OPLS. Using the amber-port is, in my opinion, the best
way to handle DNA/RNA (in GROMACS).
I fear, I can't really help you with your error, but did you try the
amber99 FF? I use that and never ran into such errors. Did you had a
look, if your total charge is more or less an integer? If not, one
proton in your first base may be the wrong type...but this shouldn't
result into your error.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
root wrote:
> Dear GROMACS user:
>
> Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
> http://folding.stanford.edu and now I understand your comments.
> We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
> desapears, but the error messages is similar.
> (Fatal error:
>>>> Atoms in the .top are not numbered consecutively from 1
>>>>
>>>> -------------------------------------------------------
>>>>
>>>> We tested the dick.top file, and we verified that the atoms
>>> are numbered
>>>> consecutively from 1 to 758.)
>
> We download the ffamber_v3.3.1-doc.tar.gz, that we considered that
> correspond to the 3.3.1 version of GROMACS.
> Is this correct?
>
> Thanks in advance.
>
> Mario
>
> El lun, 07-05-2007 a las 23:17 +0200, Erik Marklund escribió:
>> As someone already mentioned, the following can be found among the
>> AMBERport FAQ:
>>
>> >>
>> Why do I get a grompp warning "missing white space after `#define
>> proper_*'?"
>> Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these
>> warnings, which result from the use of the N* atom type of the AMBER
>> family of force fields and can be ignored.
>> <<
>>
>> Did you try doing that?
>>
>> Good luck!
>>
>> /Erik
>>
>> 7 maj 2007 kl. 22.29 skrev root:
>>
>> Hi,
>
>> I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then
>> it
>> should get rid of the warnings about "spaces are absent in target after
>> the
>> name of macro". For more info see
>> <http://folding.stanford.edu/ffamber/FAQ.html>
>
>> Tom
>
>> --On 07 May 2007 20:42 +0200 David van der Spoel
>> <spoel at xray.bmc.uu.se>
>> wrote:
>>> David and GROMACS users:
>>> Sorry we changed the error message in ...
>>>
>>> /usr/local/gromacs/share/top/ffamber03bon.itp:541:22: warning: spaces
>>> are absent in target after the name of macro
>>>
>>> because of the original message was in spanish.
>>>
>>> We checked these files above. We run GROMACS in fedora 6.0
>>> We analyzed the warning messages. They correspond to a format of
>>> description of a dihedral angle. For example the 538:22 warning
>>> correspond to le line 538 column 22
>>>
>>> #define proper_X_CT_N*_X
>>> and there are a format problem with the * symbol.
>>>
>>> we don't know that to do still with this.
>>>
>>>
>>> Thanks in advance
>>>
>>> root wrote:
>>> De:
>>> David van der Spoel
>>> <spoel at xray.bmc.uu.se>
>>> Responder a:
>>> Discussion list for GROMACS users
>>> <gmx-users at gromacs.org>
>>> Para:
>>> Discussion list for GROMACS users
>>> <gmx-users at gromacs.org>
>>> Asunto:
>>> Re: [gmx-users] Problems using
>>> grompp and amber force field
>>> Fecha:
>>> Mon, 07 May 2007 20:42:51 +0200
>>> (15:42 ART)
>>>
>>> The procedure to simulate the DNA dodecamer was:
>>>
>>> 1) We generate the DNA topology and coordinates in gromacs format
>>> (with
>>> the amber03 force field ) using the pdb2gmx program:
>>>
>>> pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce
>>>
>>> 2) and we obtain the box with the dodecamer plus water coordinates
>>> using editconf and genbox:
>>>
>>> editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle
>>> 90 90
>>> 90
>>> genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top
>>>
>>> 3) with the files dick03.pdb and dick.top we run grompp:
>>>
>>> grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
>>>
>>> The output of the program indicate
>>> ...
>>> creating statusfile for 1 node...
>>>
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
>>> checking input for internal consistency...
>>> calling /usr/bin/cpp...
>>> In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
>>> de dick.top:11:
>>> /usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
>>> warning: spaces are absent in target after the name of macro
>>> /usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
>>> warning: spaces are absent in target after the name of macro
>>> /usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
>>> warning: spaces are absent in target after the name of macro
>>> /usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
>>> warning: spaces are absent in target after the name of macro
>>> /usr/local/gromacs/share/top/ffamber03bon.itp:559:19:
>>> warning: spaces are absent in target after the name of macro
>>> processing topology...
>>>
>>> check the files above. is the error message correct? then fix
>>> it.
>>>
>>> what kind of system are you running this on?
>>>
>>>> processing topology...
>>>> Generated 2701 of the 2701 non-bonded parameter combinations
>>>> Generating 1-4 interactions: fudge = 0.5
>>>> Generated 2701 of the 2701 1-4 parameter combinations
>>>> -------------------------------------------------------
>>>> Program grompp, VERSION 3.3.1
>>>> Source code file: toppush.c, line: 758
>>>>
>>>> Fatal error:
>>>> Atoms in the .top are not numbered consecutively from 1
>>>>
>>>> -------------------------------------------------------
>>>>
>>>> We tested the dick.top file, and we verified that the atoms
>>> are numbered
>>>> consecutively from 1 to 758.
>>>> We analyzed the warning messages. They correspond to a format
>>> of
>>>> desciption of a dihedral angle. For example the 538:22 warning
>>>> correspond to le line 538 column 22
>>>>
>>>> #define proper_X_CT_N*_X
>>>> and there are a format problem with the * simbol.
>>>>
>>>> we don't know that to do still with this.
>>>>
>>>>
>>>>
>>>> Thanks in advance
>>>>
>>>> Mario Campo and Griselda Corral
>>>> Fac. de Cs. Exactas y Naturales
>>>> UNLPam
>>>>
>>>>
>>>>
>>>>
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>>>
>>> --
>>> David.
>>>
>>> ______________________________________________________________________
>>> __
>>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
>>> group,
>>> 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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>> _______________________________________________
>> Erik Marklund, PhD student
>> Laboratory of Molecular Biophysics,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: +46 18 471 4537 fax: +46 18 511 755
>> erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
>>
>>
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>
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