I am also working with steroids (but in my case, steroidal hybrid inhibitors)
with the gmx force field. From my experience working with the PRODRG program,
the topologies needed some modifications (for example the program assigns my
phenol OH as a carbonyl and one aromatic bare carbon as a CH1) and produce
strange partial charges for the steroid which are not reproduced for different
inhibitors with the same steroid moiety. Maybe you should try assigning partial
charges using a reliable method (ex with bcc in antechamber) to see if that is
the problem (but I think that is unlikely).
If you are seeing that same behavior in a steepest descent minimization step,
there can be an error in the bonding scheme (check the bonding section of your
topology) or a missing improper dihedral parameter.
Diane
-Original Message-
From: [EMAIL PROTECTED] on behalf of dhruva chakravorty
Sent: Tue 8/15/2006 6:13 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] steroid topology
Hello,
I have been having trouble with a topology I created
for androst-5-ene-3,17-dione (GROMOS 96 force field).
I have found the molecule to bend inwards withing 100
ps of equilibration, something which has not been seen
by others who have used CHARMM or AMBER. I have also
tried to convert the topology generated by the PRODRG
DUNDEE server for GROMACS but had the same issues with
it. Can anyone throw any pointers my way, or better
still a steroid topology which works
Regards
Dhruv
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