Previous Thread
Next Thread
Print Thread
About Ligand Parameters
#12150 10/24/06 08:45 AM
Joined: Jun 2006
Posts: 21
A
Forum Member
OP Offline
Forum Member
A
Joined: Jun 2006
Posts: 21
Dear all,
I could get the PSF file and CRD file of my ligand from insightII.But I do not know how to get the RTF file and PRM file of my ligand. Thanks anyone who could help me!
By the way, how to deal with the ligand which has a covalent bond with the receptor besides QM/MM?

Re: About Ligand Parameters
accelrys #12151 10/24/06 04:34 PM
Joined: Sep 2003
Posts: 8,447
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,447
Presumably, the RTF and PARAM files are provided with InSight; the Accelrys company may have some info about this on their web site.

The usual way of defining connectivity changes is via a patch residue (PRES); a common problem for ligand to amino acid covalent bonds is missing parameters. One needs to be fairly careful about the choices and testing when adding new residues and patch residues, and deailing with the parameter issues that will certainly occur.


Rick Venable
computational chemist

Re: About Ligand Parameters
rmv #12152 10/25/06 12:52 AM
Joined: Jun 2006
Posts: 21
A
Forum Member
OP Offline
Forum Member
A
Joined: Jun 2006
Posts: 21
You mean use the PATCH to connect the receptor and the ligand just like patch disulfide bonds?
e.g. patch disu 4pti 5 4pti 55
Then how to alter the script about this?
Thanks!

Re: About Ligand Parameters
accelrys #12153 10/25/06 02:53 AM
Joined: Sep 2003
Posts: 8,447
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,447
You need to find the RTF file, study the definition for 'PRES DISU' and few others, and read some documentation for starters. Then you can start to work on creating your own PRES definition, which will link the ligand to the protein. It's your work in defining the PRES which will determine the details of the PATCH command that uses it.


Rick Venable
computational chemist


Moderated by  John Legato, lennart 

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: 0.012s Queries: 22 (0.007s) Memory: 0.9113 MB (Peak: 0.9936 MB) Data Comp: Off Server Time: 2020-05-29 12:32:25 UTC
Valid HTML 5 and Valid CSS