Hi,
You have the following flag in your input file:
ntwprt=22,
This means "only write the first 22 atoms to the trajectory". You'll
need a topology to match. You can create such a "stripped" topology
with either parmed or cpptraj. E.g. (cpptraj):
parm myparm.parm7
parmstrip !(.1-22)
parmwrite out strip.myparm.parm7
Commands are similar for parmed (use the 'strip' and 'parmout'
commands instead of 'parmstrip' and 'parmwrite'). See the manual for
full details.
-Dan
On Thu, Dec 17, 2020 at 1:17 AM Sruthi Sudhakar
<sruthisudhakarraji.gmail.com> wrote:
>
> Dear all,
>
> I have done a 100 ns NVT simulation on a protein-DNA system and used the
> restart file to do 30ns gaussian accelerated MD on to the system using the
> script attached. After completion, upon running cpptraj to obtain the rmsd
> of the system using the GaMD trajectory, I got the error that there are
> only 22 atoms in the nc file while, 2,00,000 atoms in the prmtop. I had
> used the same prmtop for running the GaMD as well. Could someone suggest
> why this might be happening? I had tried to visualize but was not possible
> due to exactly the same issue.
>
> Regards,
> Sruthi Sudhakar
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Received on Thu Dec 17 2020 - 09:30:02 PST
