[gmx-users] Cofactor - Coenzyme - Enzyme Complex 2

[Tanos C. C. França]

Dear Daan, 

I didn't changed the input PDB file cause it's not mentioned in the
tutorial.
My procedure was the following:
I introduced the two molecules in the enzyme.gro and in the topology
files as described in the tutorial for Drug-Enzyme complex. First I
runned pdb2gmx with the enzyme.pdb file, without the drug, to generate
enzyme.gro and enzyme.top files. Then, I introduced the coordinates of
the drg.gro file previously generated in the site:
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html to the
enzyme.gro file. After that I added to the file enzyme.top: "#include
drg.itp" and "#include cof.itp" under the forcefield parameters and DRG
And COF under Compound and 1 for each one under # mols. When I use only
DRG there is no problem, but when I introduce COF the program don’t
recognize this molecule type. I tried instead use DRG1 and DRG2 but it
didn´t recognized DRG1 and DRG2 as molecule type too. So, how should I
name COF in a way GROMACS could recognize it ???????

Thank you very much for your attention,

Tanos C. C. Franca
IME - Rio de Janeiro - RJ
Brasil

-----Mensagem original-----
De: Daan Virtual [mailto:vdava at davapc1.bioch.dundee.ac.uk] 
Enviada em: quinta-feira, 27 de fevereiro de 2003 19:37
Para: Tanos C. C. França
Cc: gmx-users at gromacs.org
Assunto: Re: [gmx-users] Cofactor - Coenzyme - Enzyme Complex


Hi Tanos

Just checking - but did you change the name in the input PDB file *AND*
the topology file?

Daan


On Thu, 27 Feb 2003, [iso-8859-1] Tanos C. C. França wrote:

> Hi Folks !!!!!!!!
> I´m trying to build a Coenzyme – Cofactor - Enzyme complex using the
> “GROMACS Tutorial for Drug – Enzyme complex”
> As I wish to dock two different molecules to my enzyme´s active site,
I
> named then DRG (as in the tutorial) and COF. But when I run grompp,
the
> program gives me the message: “Fatal error:  not such moleculetype
> COF”. I tryed several other names to the second molecule but grompp
> always halted. So, I would like to know which moleculetype name should
I
> use that GROMACS will recognize in this case.
>
> Thanks a lot in advance.
> Tanos C. C. Franca.
> IME – Rio de Janeiro - RJ
>
>
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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

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