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#12150 - 10/24/06 04:45 AM About Ligand Parameters
accelrys Offline
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Registered: 06/21/06
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?

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#12151 - 10/24/06 12:34 PM Re: About Ligand Parameters [Re: accelrys]
rmv Offline

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Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
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


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#12152 - 10/24/06 08:52 PM Re: About Ligand Parameters [Re: rmv]
accelrys Offline
Forum Member

Registered: 06/21/06
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!

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#12153 - 10/24/06 10:53 PM Re: About Ligand Parameters [Re: accelrys]
rmv Offline

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Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
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


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