[gmx-users] GROMOS96 and protein-ligand complex

[Daan van Aalten]

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