[gmx-users] grompp error

[Daan van Aalten]

Hi Nusrat

PRODRG topologies only work with the standard ffgmx forcefield....

cheers

Daan

On Fri, 21 Dec 2001, Nusrat JM Sanghamitra wrote:

> Hi
> I am trying to to run MD for a copper complex. I have written a topology
> file for it as PRODRG server is not supporting to write it 
> I included
> "ffG43a1.itp" in it then to preprocess while i do 
> grompp-v -f em -c b4em -o em -p cuthp it is giving the
> following
> error: could any of you please go through it and suggest me the correct
> way of doing it?
> while processing topology...
> Warning 1 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 3]:
>   Overriding atomtype O
> Warning 2 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 4]:
>   Overriding atomtype OM
> Warning 3 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 5]:
>   Overriding atomtype OA
> Warning 4 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 6]:
>   Overriding atomtype OW
> Warning 5 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 7]:
>   Overriding atomtype N
> Warning 6 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 8]:
>   Overriding atomtype NT
> Warning 7 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 9]:
>   Overriding atomtype NL
> Warning 8 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 11]:
>   Overriding atomtype NZ
> Warning 9 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 12]:
>   Overriding atomtype NE
> Warning 10 [file "/usr/local/share/gromacs/top/ffG43a1nb.itp", line 13]:
>   Overriding atomtype C
> Cleaning up temporary file /tmp/fileseLzVb
> Fatal error: Too many warnings, grompp terminated
> so i removed it and included ions.itp that also gave error -----atom type
> K not found.
> I thought to remove ffG43a1nb.itp from ffG34a1.itp but i am not able to
> modify the forcefields in /usr/local/share/top directory, it says it is
> read-only.
> so i created separate itp files and tried to include in em.mdp option
> -I/home/name/my_lib but there also it is giving error.
> could any of you please help me out?
> thanks
> Nusrat.
> 
> 
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD 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!
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     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
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       O