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

[Daan van Aalten]

Hi

PRODRG and the GMX ffgmx forcefield work with the implicit hydrogen
concept for carbons. Thus, you can only modify the *explicit* hydrogen
structure (i.e. on O, N, S)

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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