AW: Peptide planarity Dihedral angle restraints

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Dec 09 2011 - 00:18:47 CST

Hi,

 

wouldn't extrabonds help you

 

Good luck

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Aron Broom
Gesendet: Freitag, 9. Dezember 2011 04:11
An: Boyang Wang
Cc: Vijay Vammi; namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Peptide planarity Dihedral angle restraints

 

Santosh,

I may be misunderstanding, but couldn't you just write a script that would
identify (or look through your coordinate file manually) the atom numbers
for the X-C-N-X atoms that make up the backbone, and then apply a harmonic
restraint for each? It would be a large restraint file no doubt, and
applying so many restraints might slow performance a bit.

~Aron

On Thu, Dec 8, 2011 at 9:17 PM, Boyang Wang <pkuwangboyang_at_gmail.com> wrote:

Hi Santhosh,

 

I agree. There are a limited number of impropers and you can try. It takes a
long time to find out all the impropers and you need the connections with
them. There is not a standard way of doing this.

 

Boyang

On Fri, Dec 9, 2011 at 10:07 AM, Vijay Vammi <vsvammi_at_iastate.edu> wrote:

Hello all,

 

During MD simulation, I want to put additional restraints to maintain
peptide planarity.

In AMBER forcefields, i was able to do it by increasing the Kchi value for
X-C-N-X. (in the parm99.dat).

 

In CHARMM forcefields, as far as I know, wildcards would be accepted only if
there is no specific combination found. One way of solving this would be to

1). For every peptide bond, find all the atomtypes combination(eg: CA-C-N-CA
could be CT1-C-N-CT1 and many other possibilities) and increase the Kchi
value in the parameter file.

 

Is there any other simple way?

Thanks

Santhosh

-- 
Boyang Wang, Ph.D.
 

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