Previous Thread
Next Thread
Print Thread
parameters wanted
#11798 09/20/06 11:57 PM
Joined: Oct 2003
Posts: 39
Forum Member
OP Offline
Forum Member
Joined: Oct 2003
Posts: 39
Hi,

Would you like to give your suggestions/hints about the methylated lysine, in particular, the angle parameter of CE (CT2) - NZ - C (Methyl, CT3?)? Thanks you in advance.

Re: parameters wanted
zhangxd68 #11799 09/23/06 06:00 PM
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782

i don't think a protonated secondary amine has been studied. do a quick QM calculation on protonated dimethylamine and assign the needed parameter based on the optimized structure. be sure to check that the angle parameters you determine yield the QM angle in the charmm optimized structure.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: parameters wanted
alex #11800 09/24/06 02:21 AM
Joined: Aug 2006
Posts: 6
D
Forum Member
Offline
Forum Member
D
Joined: Aug 2006
Posts: 6
Hi all
does any one have topology and parameter file for deprotonated form of proline amino acid. whatever i am getting from www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm is for zwiterionic form of proline residue.

Re: parameters wanted
Dhiraj #11801 09/25/06 06:07 PM
Joined: Sep 2003
Posts: 8,506
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,506
It should be noted that all amino acids are described as polymer residues with implied bonds to the i-1 and i+1 residues. The terminal patches applied with the GENErate command determine how the N-term amine and C-term CO2 are modified wrt. the assumed amide linkage. The default patches create the zwitterion form, which is usually correct in the physiological pH range. If one wishes to study more extreme pH conditions, careful study of the protein topology files, including the 'model' file in the toppar/stream subdir, should allow one to create a new patch based on the standard PROP patch (and the model TP2 residue) that is not protonated.


Rick Venable
computational chemist


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: 0.013s Queries: 22 (0.006s) Memory: 0.9126 MB (Peak: 0.9958 MB) Data Comp: Off Server Time: 2020-10-29 08:05:36 UTC
Valid HTML 5 and Valid CSS