Re: [gmx-users] Problems using grompp and amber force field

Tue, 08 May 2007 00:39:09 -0700

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

<[EMAIL PROTECTED]> 
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
<[EMAIL PROTECTED]>
                       Responder a:
Discussion list for GROMACS users
<gmx-users@gromacs.org>
                              Para:
Discussion list for GROMACS users
<gmx-users@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
        [EMAIL PROTECTED]    [EMAIL PROTECTED]
        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
[EMAIL PROTECTED]       http://xray.bmc.uu.se/molbiophys


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