Previous Thread
Next Thread
Print Thread
doxorubicin charmm topology
#34655 12/18/14 07:26 PM
Joined: Oct 2005
Posts: 206
P
prakash Offline OP
Forum Member
OP Offline
Forum Member
P
Joined: Oct 2005
Posts: 206
Are there exisiting doxorubicin topology in charmm, I have the Gromacs one, are there any top and param converting tool for CHARMM from GROMACS.

Re: doxorubicin charmm topology
prakash #34679 12/29/14 02:56 PM
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782

Have you tried obtaining parameters from CGenFF/Paramchem? Doxorubicin contains a sugar so you may want to obtain the parameters for the sugar moiety from the C36 carbohydrate FF and the remainder from CGenFF.

Note that one should not mix parameters from different force fields. Thus, it is not recommneded to use Gromacs parameters with the CHARMM biological force field.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.011s Queries: 18 (0.006s) Memory: 0.8935 MB (Peak: 0.9601 MB) Data Comp: Off Server Time: 2021-05-06 15:08:18 UTC
Valid HTML 5 and Valid CSS