Sir,
I was following the protocol given in the below mentioned link to learn MD
simulation of docked structures. In this link, it is given to develop file
from H++. If this is not the right procedure please inform me what can I do
to perform MD simulation for docked structures including ions also as
protein cofactors.
http://ambermd.org/tutorials/pengfei/index.htm
On Mon, Jan 29, 2018 at 6:42 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Jan 29, 2018, SHALJA VERMA wrote:
>
> > I am using this command to generate protein PDB from the files received
> > from H++ but the generated PDB is empty. Please help me how to come out
> of
> > this problem.
> >
> > ambpdb -p 0.15_80_10_pH6.5_1ODX.top -c 0.15_80_10_pH6.5_1ODX.crd >
> > 0.15_80_10_pH6.5_1ODX.pdb
>
> I'm confused: *.top and *.crd files are created by LEaP, and not by H++.
> What
> is the "file received from H++"?
>
> What is the result of typing "head 0.15_80_10_pH6.5_1ODX.top"? The first
> integer should be the number of atoms. Does that look correct?
>
> ....dac
>
>
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Received on Mon Jan 29 2018 - 06:00:03 PST
