Re: [AMBER] ambpdb error while conversion

From: Sunita Patel <>
Date: Tue, 24 Sep 2019 16:42:54 +0530

Dear David,

I am using Amber18 and AmberTool18. I generated *.prmtop file using ff14SB
force field.
source leaprc.protein.ff14SB
m = loadpdb AH_noH.pdb
saveamberparm m AH_ff14SB.prmtop AH_ff14SB.inpcrd
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
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.


On Fri, Sep 20, 2019 at 6:45 PM David Case <> 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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Received on Tue Sep 24 2019 - 04:30:02 PDT
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