On 2/3/13 1:01 AM, James Starlight wrote:
Justin,

thanks again for suggestions.

I'm not quite sure how I can use tpbconv -zeroq. For example I want to
reduce charges of all amino acids except Asp Glu and His ( to monitor
s.b dynamics between that groups only).

As I understood -zeroq working with the groups defined in the index
file so I should just  select all residues that I need in that file,
shouldnt it  ? Also doest it possible to select pairs of residues

Yes.

placed in the sequence on the distant sites ? (e.g by selecting only
pairs within some range of n1 and n2+k where k>n1+10)


I don't understand what you mean. tpbconv will only take one index group for zeroing charges, so I don't understand how such a relative scheme would work for all cases.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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