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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