hello
you would want to check the validity of the new prmtop file after adding
CMAP parameters using parmed,
See the following commands
source $AMBERHOME/amber.sh
parmed AH_leap_struct_CMAP.prmtop
checkValidity
If the prmtop file is corrupted while adding CMAP parameters parmed will
tell.
Best Regards
On Thu, 19 Sep 2019 at 17:01, Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> Dear Users,
>
> We are trying to convert *.prmtop and *.rst files obtained after energy
> minimization into a pdb file using ambpdb command. The *.prmtop file is
> obtained by adding extra CMAP parameters (FF14IDPSFF) to the original
> prmtop file obtained from FF14SB force field. However, we got the following
> error message.
>
> ambpdb -p AH_leap_struct_CMAP.prmtop -c AH_struct_min.rst >
> AH_struct_min.pdb
> Segmentation fault (core dumped)
>
> When we are converting the prmtop file to pdb without adding CMAP
> parameters, we could successfully do that without any error.
> How can we get the pdb file by using the prmtop file with the CMAP
> parameters?
>
> Sincerely,
> Sunita
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Received on Thu Sep 19 2019 - 05:00:03 PDT
