Re: [AMBER] nc files contain lesser number of atoms compared to prmtop

From: Daniel Roe <>
Date: Thu, 17 Dec 2020 12:03:26 -0500


You have the following flag in your input file:


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.


On Thu, Dec 17, 2020 at 1:17 AM Sruthi Sudhakar
<> 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
> _______________________________________________
> AMBER mailing list

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Received on Thu Dec 17 2020 - 09:30:02 PST
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