On 10/7/13 10:46 AM, bipin singh wrote:
Hello All,
I have calculated the distance between the binding pocket of protein and
the ligand molecule but due to ligand diffusion out of box, I am getting
wrong distance as first it increases till 5nm and then decrease again to
around 1nm during the simulation (which is not possible).
I have fitted my trajectory with using trjconv -pbc mol -ur compact -center
(protein) option.
I have also tried the -nojump option but getting the same results for
distances.
Please suggest how to get the real distance without the PBC effect.
It sounds like that very well could be the real distance. If the ligand
diffused out, it simply becomes part of the solvent around the protein and can
diffuse around freely.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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