On 10/31/13 7:03 PM, Ehsan Sadeghi wrote:
Thanks Justin,
Here is the steps that I followed:
pdb2gmx -f eth.pdb -o eth.gro -p eth.top
pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top
editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5
genbox -cp box.gro -cs spc216.gro -ci eth.gro -nmol 1000 -o solvated.gro
I got the box with ionomer in ethanol and water solution. However, I only have
400 of eth and 423 water molecule. The box wasn't large enough?
Follow the advice at the link I posted before. Trying to add ethanol while
simultaneously solvating is a bad idea. If genbox cannot add 1000 ethanol
molecules without trying to do anything else, then yes, the box is simply too
small. At this point, we can't say because it could simply be that simultaneous
solvation might have been competing for available box volume.
What should I do with .top file? I have the .top file for ionomer and .top file
for one eth molecule.
It is simple to covert between .top and .itp and #include them however you see
fit. Probably the conceptually easiest methhod is to consider ethanol just like
any other solvent (i.e. water) and #include it within the .top for the ionomer,
which is just like any other solute.
-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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