[gmx-users] Dynamics of the salt-bridges
jalemkul at vt.edu
Sun Feb 3 18:06:06 CET 2013
On 2/3/13 1:01 AM, James Starlight wrote:
> 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
> 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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users