[gmx-users] steroid topology
diane.fournier at crchul.ulaval.ca
Wed Aug 16 17:53:00 CEST 2006
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.
From: gmx-users-bounces at gromacs.org on behalf of dhruva chakravorty
Sent: Tue 8/15/2006 6:13 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] steroid topology
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
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