[gmx-users] Re: Two questions when simulate the protein in lipid bilayer: 1. ratio of water/lipid; 2. ligand charge

[Daan van Aalten]

.... and apart from the fact it wont work on carbons, also your ADDHYD
command is incorrect - if you say "ADDHYD C" how on earth is PRODRG to
know which of the carbons (named CAA ... CAF) you mean ??

Daan

On Sat, 14 Jun 2003, PeiQuan Chen wrote:

> Dear gmx-users-request:
>
>
> Daan wrote:
> >
> >PRODRG now includes an algorithm which "distributes" formal charges over
> >atoms in the molecule according to their relative electronegativities.
> >On a test set of molecules, this approach gives an RMSD of (only) 0.1
> >electron compared to charges calculated on the same test set of molecules
> >with GAMESS.
> >
> >However - it is important to ensure protonation is correct, you can
> >correct that with ADDHYD/DELHYD (see faq) commands *at the end* of your
> >input file.
>    I really want to know how to make a topol file of all-atom benzen. I think I can
> use the ADDHYD commnads to implement it.
>
> But when I input the follows, I got the error:
>
> (ERRDRG> Atom C     referenced in instruction was not found.
> PRODRG> Drug topology not made, sorry!)
>
> HETATM    1  CAA DRG     1       0.590   2.790  -0.010  1.00 20.00             C
> HETATM    2  CAB DRG     1       0.580   1.370   0.000  1.00 20.00             C
> HETATM    3  CAD DRG     1       1.810   0.660   0.010  1.00 20.00             C
> HETATM    4  CAF DRG     1       3.040   1.370   0.010  1.00 20.00             C
> HETATM    5  CAE DRG     1       3.040   2.790   0.000  1.00 20.00             C
> HETATM    6  CAC DRG     1       1.810   3.490  -0.010  1.00 20.00             C
> END
> ADDHYD C
>
>
> Sincerely yours
> ----
> PeiQuan Chen
> ________________________________________________________________________
> PeiQuan Chen 	Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone:	(86)2223506728		Mobile Phone: (+86)13920675030
> gromacs at 163.com
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
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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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