[AMBER] chamber problem

From: Prabir Khatua <prabir07chem.gmail.com>
Date: Wed, 6 Feb 2019 03:16:38 +0530

Dear all,

I am trying to create prmtop file from charmm formatted psf file by chamber
the calculation mmpbsa. I am using following command to do it.

/home/prabir/SOFTWARE/AMBER/AMBER14/amber14/bin/chamber -cmap -top
top_all36_prot.rtf -param par_all36_prot.prm -str toppar_water_ions.str
top_all36_carb.rtf par_all36_carb.prm -xpsf Willbold_IRF_1-42_6X2.psf -crd
Willbold_IRF_1-42_6X2.pdb -p prot.prmtop -inpcrd prot.inpcrd

However, I am getting following error.
<get_atom_parameters>ERROR atom with mass 1 has type alreadydesignated as
non-hydrogen type
 <get_atom_parameters> atom 2 1.0080000000000000 HT1
 Cannot continue

Despite adding some of the stream files by -str option as found in amber
mailing list, the problem is still not fixed. Please note that during
preparation of psf file, I needed only par_all36_prot.prm and
top_all36_prot.rtf file. Thus, I have no clue which specific file I need to
add. Can anyone please suggest me how to check it which file to be added?

I have one more query. CHAMBER is not allowing me to run this command
without mentioning cmap option. Thus, tt seems to be mandatory. I am not
sure whether I should turn on cmap or not for charmm36. Please suggest me
what to do. Any suggestion would be appreciated.

Thank you,


*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*
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Received on Tue Feb 05 2019 - 14:00:02 PST
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