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

[Daan van Aalten]

Hi PeiQuan

We have deliberately increased the force constants on the impropers
10-fold to make the geometry of GMX mimimized molecules better agree
with known small molecule structures from the CSD.
In fact we are considering introducing an entirely new set of forcefield
constants based on small molecule crystal structure databases.

cheers

Daan

On Sat, 14 Jun 2003, PeiQuan Chen wrote:

> Dear Daan van Aalten:
>
>   Thank you for kind help.
>   But I have something confused with the topol files generated by PRODRG.
> The dihedrals parameters I get from the PRODRG is following:
>  [ dihedrals ]
>  ;ai  aj  ak  al  fu    c0    c1 m  c0   c1 m
>    1   2   3   4   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAA  CAB  CAD  CAF
>    2   3   4   5   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAB  CAD  CAF  CAE
>    3   4   5   6   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAD  CAF  CAE  CAC
>    4   5   6   1   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAF  CAE  CAC  CAA
>    5   6   1   2   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAE  CAC  CAA  CAB
>    6   1   2   3   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAC  CAA  CAB  CAD
>
> But From the ffgmxbon.itp, I have found that:
> [ dihedraltypes ]
>   ; i    l func        q0          cq
>  CR61 CR61    2     0.000     167.360
>
>    So the topol files generated by PRODRG is not consistent with the ffgmxbon.itp. Is it a bugs?
>
>
> 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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