In the working case you specified a coordinate file following -c for
ambpdb, but in the non working case you have given it a prmtop file after
-c. You should give it the file name for your minimized restart file.
On Tue, Sep 24, 2019, 7:18 AM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> Dear David,
>
> I am using Amber18 and AmberTool18. I generated *.prmtop file using ff14SB
> force field.
> -------------------tleap.in-------
> source leaprc.protein.ff14SB
> m = loadpdb AH_noH.pdb
> saveamberparm m AH_ff14SB.prmtop AH_ff14SB.inpcrd
> quit
> ---------
> Following that we ran the perl script to add CMAP parameter into prmtop
> file which we got from the author.
> perl ./Trans_FF_IDPs -p AH_ff14SB.prmtop -o AH_ff14SB_CMAP.prmtop -c
> CMAP_parameter_ff14IDPSFF
> -------
> Then tried doing ambpdb in the following way. We succeed in generating PDB
> file when we used original *.prmtop file but got following error when used
> *CMAP.prmtop file. We were trying to generate PDB file after energy
> minimization. But to verify whether CMAP parameters addition creating the
> problem, we tried with before and after CMAP added prmtop file and we got
> following error.
>
> ambpdb -p AH_ff14SB.prmtop -c AH_ff14SB.inpcrd > test.pdb (No error)
>
> ambpdb -p AH_ff14SB.prmtop -c AH_ff14SB_CMAP.prmtop > test.pdb
> Error: Could not determine trajectory AH_ff14SB_CMAP.prmtop format.
>
> Thanks for your time and help.
>
> Sincerely,
> Sunita
>
> On Fri, Sep 20, 2019 at 6:45 PM David Case <david.case.rutgers.edu> wrote:
>
> > On Thu, Sep 19, 2019, Sunita Patel wrote:
> > >
> > >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.
> >
> > There is in principle no reason why ambpdb should have any problems with
> > prmtop files that contain CMAP parameters. It is possible that
> > something went wrong when you added the CMAP parameters (how did you do
> > that?) If you can post a small example that illustrates the problem,
> > we can try to track things down.
> >
> > Or, compare your prmtop to that in
> > AMBERHOME/AmberTools/test/chamber/dhfr_cmap_pbc. ambpdb works fine for
> > me on those files.
> >
> > ...good luck...dac
> >
> >
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> >
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Received on Tue Sep 24 2019 - 04:30:03 PDT
