[gmx-users] PRODRG again

[Osmany Guirola Cruz]

I have a "drug" greater than 300 atoms what should I do to get the
topology
I don know if exist another program or server that do something similar 
My drug have 310 atoms 
Help please  :-(




-----Original Message-----
From: Daan van Aalten [mailto:vdava at davapc1.bioch.dundee.ac.uk] 
Sent: Wednesday, May 19, 2004 9:58 AM
To: Peter Zoon
Cc: Discussion list for GROMACS users
Subject: Re: [gmx-users] PRODRG



Peter

You are confusing topology with conformation. For each bond between a
pair of atoms there is a choice of several hundreds of bond types, which
are associated with a) specific force constants and b) specific
equilibrium values (i.e. bond lengths). Same for bond angles. You can
minimize coordinates, but the topology stays the same.

Writing out a G96 FF topology is probably only a day's work if I can
have a full day's use of a G96 FF guru for advice and testing - and of
course everyone is busy!

cheers

Daan

On Wed, 19 May 2004, Peter Zoon wrote:

> >The atom types aren't the problem but the manual conversion of 
> >bonds/angles/dihedrals to G96 types. IMHO this may be intricate in 
> >some cases. I guess it would be very nice to have a G96 topology 
> >automatically generated by PRODRG, the GMX force field seems to be 
> >considered rather outdated even by the Gromacs crew themselves.
>
> That doesn't matter right?
> If you do a minimization (after you changed to the right atom-types), 
> the system will just equilibrate and you will reach the right topology

> automatically.
>
> Or am I making a reasoning error here?
>
> Peter
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org 
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
>


########################################################################
######
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow /
Reader
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: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW:
http://davapc1.bioch.dundee.ac.uk

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.