From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Aug 22 2013 - 22:30:11 CDT
I agree with Norman. Assuming you're using academic CHARMM (with a big M),
the experts on the CHARMM forums will be happy to help you. Here's the
forum for system setup questions:
Commercial CHARMm (with a small m) is supported by Accelrys.
If you're looking for CHARMM force field parameters for uncommon chemical
groups (regardless of which software you're using), your best bet is the
parameters set discussion forum:
Just remember the people on that forum will only help you with obtaining
the right force field, not with using it with your specific software.
Last but not least, if you're planning to use a CHARMM forum, take some
time to read the sticky topics for that forum, especially the "READ THIS
FIRST" and "READ BEFORE POSTING".
On 08/22/2013 05:39 AM, Norman Geist wrote:
> 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 [mailto:rasti_at_ut.ac.ir]
> *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:*owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *rasti
> *Gesendet:* Donnerstag, 22. August 2013 00:19
> *An:* namd-l_at_ks.uiuc.edu
> *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?
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