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: [email protected] 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 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
<<winmail.dat>>
_______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
