Hello,
It happened to me, you can use parmed to generate a new topology file
which matches your trajectory files.
Run it as: parmed -p input.prmtop -c input.inpcrd -i parmed.in
In parmed.in, you can add:
strip .8874-9999999
outparm input2.prmtop input2.inpcrd
input2.prmtop should match your trajectory!
All the best,
Qinghua
On 8/16/20 6:00 AM, 李奕言 wrote:
> Dear all,
>
> I have been running a 500 ns aMD simulation of a protein-membrane system, using ntwprt = 8873 to record only the protein atoms into the crd files.
>
> While analyzing the trajectories in cpptraj, I got the following message:
>
> Error: Number of atoms in NetCDF file NPTproductionAMD.crd (8873) does not match number in associated parmtop (95096)!
>
> I tried to delete the non-protein atoms in the original pdb file and to regenerate a protein-only parm file, yet unfortunately I miscounted the number of atoms in the protein (8872) and an 8873 number of atoms resulted in a system of the entire protein plus a single carbon atom of the POPC lipid, which was automatically converted to a full POPC molecule by Leap. It seemed that the parm file with the corresponding 8873 atoms was not available for me.
>
> Is there any way to fix it?
>
> Thanks in advance!
>
>
>
>
> Best regards,
>
> Ian
>
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Received on Sun Aug 16 2020 - 02:30:02 PDT
