[gmx-users] Monte Carlo MD & PRODRG

[Daan Virtual]

Hi John

Thanks for pointing this out - in fact PRODRG contains several other
limitations at the moment (e.g. problems with hydrogens on aromatic
nitrogens) and it is recommended that people always check by hand as far
as possible. Even if some of the charges or other parameters are not
completely correct, a PRODRG topology is a useful framework saving a lot
of time.

cheers

Daan

On Mon, 9 Sep 2002, John Kerrigan wrote:

> tion for GROMACS?  Do I have to somehow
> >> generate a PDB or a GRO file format from the final Monte Carlo
> >> configuration?  And if so, does anyone know how?
> >You need a starting conformation somehow. pdb is fine, most programs can
> >write those. Furthermore you need to make a topology. Check the prodrg
>
> Might I also caution you about the results from PRODRG.  Be careful to
> check the atom types and charges.  Especially the charges/charge groups.
> PRODRG often misses entire charge groups.
>
> Cheers!
>
> John
>
>
> *****************************************
> John E. Kerrigan, Ph.D.
> Department of Pharmacology
> University of Medicine and Dentistry of NJ
> 675 Hoes Lane
> Piscataway, NJ 08854
>
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>
> http://www2.umdnj.edu/~kerrigje
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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

        O     C           O     C         Visit the PRODRG server to take
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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
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