[AMBER] charmm psf to amber prmtop conversion problem

From: Prabir Khatua <prabir07chem.gmail.com>
Date: Mon, 11 Feb 2019 15:09:31 -0600

Dear all,

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

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

However, I am getting the 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

The problem is not fixed despite adding some of the stream files by -str
option (-str toppar_water_ions.str top_all36_carb.rtf par_all36_carb.prm)
to the above command. 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 and fix this problem?

I have one more query. CHAMBER is not allowing me to run this command
without mentioning cmap option. Thus, it 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 Mon Feb 11 2019 - 13:30:03 PST
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