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
===========================================================
<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 Wed Nov 19 2014 - 22:30:02 PST
