Hi Hirdesh, I agree with Carlos
In regards to your protein being outside the box, this may because you are
using periodic boundary conditions and to use cpptraj to account for the
PBC before viewing the trajectory - I am not sure if you have done this yet.
These commands might help ,
create a file called cpptraj,in
#!/bin/bash
date
cat <<eof > in
trajin 'simulationFileName.crd' 1 -1 1
unwrap !(:WAT)
center mass origin !(:WAT)
autoimage origin familiar
rams first mass !(:WAT)
trajout 'correctedTrajFileName.crd'
eof
cpptraj 'topologyFile.top' < in > out
echo Completed post-processing
date
on the command line type,
chmod +x cpptraj.in
./cpptraj.in
Additional information can be found here (if you are using Amber14)
http://ambermd.org/doc12/Amber14.pdf
Search for 'cpptraj.in' in the manual
hope this helps,
~K
~Kenneth
Kenneth N. McGuinness Ph.D
Research Associate
Advanced Science Research Center CUNY
Adviser: Dr. Rein Ulijn <http://www.ulijnlab.com/>
Cell: 928-925-7693
On Mon, May 2, 2016 at 8:11 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> that error is probably not related to the wrapping.
> Have you looked at the prod3.rst file to make sure it exists and is not
> currupted?
> if you want help with file issues, also send the scripts that show the file
> names for each step.
>
> On Mon, May 2, 2016 at 7:57 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
>
> > I did all atom simulation of my protein-ligand complex on 2 GPUs (Tesla
> > M2090). Here is my input file:
> >
> > All atom simulation
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 2,
> > ntp = 1,
> > cut = 8.0,
> > ntc = 2,
> > ntf = 2,
> > tempi = 298.0,
> > temp0 = 298.0,
> > ntt = 3,
> > taup = 2,
> > ig = 47123,
> > iwrap = 1,
> > gamma_ln = 1.0,
> > nstlim = 35000000, dt = 0.002
> > ntpr = 1000, ntwx = 1000, ntwr = 50000
> > &end
> >
> >
> > After 13399000 steps, simulation stopped and I got following error in
> > output file:
> >
> > "Unit 16 Error on OPEN: prod3.rst"
> >
> > When I generated the pdb file using ambpdb, I observed that proteins are
> > ligands are outside the water-box (see attached image).
> >
> > Can anyone suggest me what am I doing wrong.
> >
> >
> >
> >
> >
> > *​Thanks,Hirdesh​*
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Mon May 02 2016 - 07:00:03 PDT
