AW: AW: hi every body,

From: Norman Geist (
Date: Thu Aug 22 2013 - 04:39:38 CDT

I haven’t much experience with charm inputs so I can only suggest to check the manual of psfgen to find out to apply the patch you need. Additionally, this seems to be a VMD or CHARMm question, so this might be the wrong forum.


Good luck.


Norman Geist.


Von: rasti []
Gesendet: Donnerstag, 22. August 2013 10:03
An: Norman Geist
Betreff: Re: AW: namd-l: hi every body,


Dear Norman,


i am using charm and trying to build a psf but i have kept failing. i think it has sth to do with the top file iam using and it dose not cover the methylated Ala

thank you so much for your help,


On 2013-08-22 11:46, Norman Geist wrote:



1st of all, what kind of inputs do you use charm(psf/pdb) or amber(top/crd), or otherwise vmd or xleap/tleap ?


Norman Geist.


Von: [] Im Auftrag von rasti
Gesendet: Donnerstag, 22. August 2013 00:19
Betreff: namd-l: hi every body,


i used to apply Amber for running my simulations and i have recently started using NAMD so iam really new to this.

the structure iam working with, has got an unusual residue (methylated Val) and i think it makes the top/par files not to work ... my be there is a patch missing??

how can i add one to substitute the NH of Val with methyl?







This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:33 CST