Dear Jason,
Thankyoui for the reply, here is the old thread, I am trying to convert my files to amber format using CHAMBER, but everytime I am getting same error as mentioned in my first email. Could you please help me to solve this, I am stuck to this problem.
thanks in advance
Abhi
From: Robin Betz <robin.robinbetz.com<mailto:robin.robinbetz.com?Subject=Re%3A%20%5BAMBER%5D%20Error%20in%20CHAMBER%20output>>
Date: Wed, 19 Nov 2014 22:23:33 -0800
Hi Abhi,
Often this error message indicates that not all CHARMM parameters were
provided for this molecule.
In your case, you need to indicate additional parameter files with the -str
option, not the -param option. Run chamber --help to get a full description
of all the command line options for a complete explanation.
Hope this helps,
Robin
On Wed, Nov 19, 2014 at 10:18 PM, Abhishek TYAGI <atyagiaa.connect.ust.hk>
wrote:
> Hello AMBER People,
>
> I am using AMBERTOOL 14.
>
> The problem in CHAMBER to convert psf and pdb file to AMBER acceptable
> files, I have done following approach: My system is composed of first
> molecule-dna-water and file name is "ionized"
>
> A). When I tried following command: the first.inp and first.prm are
> parameter for first molecule.
>
> 1. $AMBERHOME/home/cbme/amber14/bin/chamber -top top_first.inp -top
> top_all36_na.rtf -param par_all27_first.prm -param par_all36_na.prm -xpsf
> ionized.psf -crd ionized.pdb -p 3.prmtop -inpcrd 3.inpcrd -nocmap
>
> Output:
> <get_atom_parameters>ERROR atom with mass 1 has type alreadydesignated as
> non-hydrogen type
> <get_atom_parameters> atom 4585 1.0080000000000000 H1
> Cannot continue
>
>
> 2. Than I added one more file with water ions information than it appears:
> $AMBERHOME/home/cbme/amber14/bin/chamber -top top_first.inp -top
> top_all36_na.rtf -param par_all27_first.prm -param par_all36_na.prm -xpsf
> ionized.psf -crd ionized.pdb -p 3.prmtop -inpcrd 3.inpcrd -nocmap -top
> toppar_water_ions.str
>
> Output:
>
> <get_atom_parameters>ERROR atom with mass >1 has type alreadydesignated
> as non-hydrogen type
> <get_atom_parameters> atom 2 15.999400000000000 O5'
> Cannot continue
>
> B). When I tried for only dna the conversion is as follows:
>
> ===========================================================
> Created prmtop summary
> ===========================================================
>
> Number of bonds with hydrogen: 236
> Number of bonds without hydrogen: 458
>
> Number of angles with hydrogen: 557
> Number of angles without hydrogen: 700
>
> Number of dihedrals with hydrogen: 930
> Number of dihedrals without hydrogen: 1334
> ===========================================================
>
> Determining filetype of coordinate file: ssdna.pdb
> Assuming PDB File.
>
>
> <write_prmtop_header> NPHB 0
> | Conversion carried out in 0.04 seconds
>
> C). When tried with my first molecule the conversion is as follows:
>
> ===========================================================
> Created prmtop summary
> ===========================================================
>
> Number of bonds with hydrogen: 0
> Number of bonds without hydrogen: 5815
>
> Number of angles with hydrogen: 0
> Number of angles without hydrogen: 11454
>
> Number of dihedrals with hydrogen: 0
> Number of dihedrals without hydrogen: 22605
> ===========================================================
>
> Determining filetype of coordinate file: first.pdb
> Assuming PDB File.
> <write_prmtop_header> make_exclusion_list reallocating 62976
>
>
> <write_prmtop_header> NPHB 0
> | Conversion carried out in 0.98 seconds
>
> D). For dry system first molecule-dna the output is as follows:
>
> ===========================================================
> PSF input parsing summary
> ===========================================================
>
> Number of PSF flags found: 1
>
> Number of atoms found: 4583
> Number of residues found: 3957
>
> Number of bonds found: 6509
> Number of angles found: 12711
> Number of dihedrals found: 24429
> Number of impropers found: 57
>
> Number of donors found: 0
> Number of acceptors found: 0
> Number of explicit nonbonded exclusions found: 0
>
> Number of groups found: 1
>
> ===========================================================
>
From: Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20AMBER%20Digest%2C%20Vol%201044%2C%20Issue%201>>
Date: Mon, 24 Nov 2014 05:44:31 -0500
On Mon, Nov 24, 2014 at 1:08 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk>
wrote:
> Hello Robin,
>
> Thankyou for the reply, but I tried with -str format but still I am
> getting the same error
>
?Respond to the actual thread where this issue was being discussed, not the
digest. I can't get any context about your original problem when the email
is flooded with dozens of irrelevant threads.
All the best,
Jason
?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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> <get_atom_parameters> ERROR, topology file(s) ends without finding all
> atom types,
> number found: 33 needed ntypes: 34
> Exiting
> ===========================================================
>
>
>
> The final thing I got is the first molecule and dna files are constructed
> but my solvated model and dry model files are not converted.
>
> I am not understanding where is the problem.
>
> I hope you understand what I want to ask, I am new to AMBER.
>
> Thanks in advance
>
> regards
> Abhi
>
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Received on Mon Nov 24 2014 - 21:00:02 PST
