[gmx-users] GROMOS96 and protein-ligand complex

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Wed Sep 24 13:17:00 CEST 2003


Dear Outi,
I have the same problem some time ago.
What I did then was to generate the topology with PRODRG for GROMOS87 
and then convert it to GROMOS96 by hand (you have to use the paramenters 
in the itp file of GROMOS87/96). It´s really tedious but it works
Hope this help
Good luck!
Regards
Ruben
Daan van Aalten wrote:

>you cannot use the PRODRG topologies with anything else than the ffgmx
>force field
>
>On Mon, 22 Sep 2003, Outi Maija Salo wrote:
>
>  
>
>>Hi!
>>
>>
>>We have some problems in preparing a normal MD run for a protein-ligand
>>complex.
>>We prepared the ligand .itp and .gro files in PRODRG server.
>>THen we added these files to corresponding .gro file and .top file of the
>>protein just as we have previously done and it worked then.
>>
>>We chose to use the GROMOS96(ffG43a1) force field (this was new to
>>previous work).
>>
>>The first problem occurred when we tried to use grompp:
>>
>>Fatal error: Atomtype 'CR61' not found!
>>
>>Well, this atom type was not in ffG43a1.atp. So, we changed this and some
>>other atom types to the corresponding types of this force field.
>>
>>Our ligand has the name LIG.
>>The next error message from grompp was the following:
>>
>>
>> WARNING 2 [file "top_ligand.top", line 18689]:
>>  atom C35 (Res LIG-301) has mass 0
>>
>>WARNING 3 [file "top_ligand.top", line 18689]:
>>  atom C34 (Res LIG-301) has mass 0
>>
>>WARNING 4 [file "top_ligand.top", line 18689]:
>>  atom C33 (Res LIG-301) has mass 0
>>
>>WARNING 5 [file "top_ligand.top", line 18689]:
>>  atom O36 (Res LIG-301) has mass 0
>>
>>WARNING 6 [file "top_ligand.top", line 18689]:
>>  atom HAA (Res LIG-301) has mass 0
>>
>>WARNING 7 [file "top_ligand.top", line 18689]:
>>  atom C32 (Res LIG-301) has mass 0
>>
>>WARNING 8 [file "top_ligand.top", line 18689]:
>>  atom C31 (Res LIG-301) has mass 0
>>
>>WARNING 9 [file "top_ligand.top", line 18689]:
>>  atom C30 (Res LIG-301) has mass 0
>>
>>WARNING 10 [file "top_ligand.top", line 18689]:
>>  atom C29 (Res LIG-301) has mass 0
>>
>>...
>>
>>What is the problem? Is the GROMOS96 ff not suitable for protein-ligand
>>complexes or should we change some ff parameters e.g. in ffG43a1nb.itp
>>file? We really could not find the reason for this...
>>
>>Thanks for your help!
>>
>>Outi Salo
>>University of Kuopio
>>Finland
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>>    
>>
>
>
>##############################################################################
>
>Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
>Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
>Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
>School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
>Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk
>
>        O     C           O     C         Visit the PRODRG server to take
>        "     |           "     |         the stress out of your topologies!
>  N--c--C--N--C--C--N--C--C--N--C--C--O
>     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
>     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
>       "
>       O
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