Dear Amberists,
I am trying to convert an AMBER topology to to GROMACS using amb2gmx.py.
But I get this error during running. Can some one point out whats the
problem in this case. Also amb2gmx seems to work fine with Amber 11 but as
I generated PDB with TIP4Pew and FF14SB hence unfortumnately I will not
able to reproduce the trajectory. Is there any way to fix this issue with
amb2gmx in AmberTools15.
| ambpdb (C++) Version V15.00
Error: Option '-atm' is not yet supported.
Parsing PDB file gmx.pdb...
found:
0 protein residues
0 sodium ions
0 chloride ions
0 waters
Use of uninitialized value $ntotalres in printf at /home/sbhakat/bin/
amb2gmx.pl line 263.
0 TOTAL residues read
Reading prmtop file...
0 atom type indices read.
LJ 1 0.3250 0.7113
LJ 2 0.1069 0.0657
LJ 3 0.3400 0.4577
LJ 4 0.1960 0.0657
LJ 5 0.2650 0.0657
LJ 6 0.3400 0.3598
LJ 7 0.2960 0.8786
LJ 8 0.2471 0.0657
LJ 9 0.3066 0.8803
LJ 10 0.0000 0.0000
LJ 11 0.2600 0.0628
LJ 12 0.3564 1.0460
LJ 13 0.2511 0.0628
LJ 14 0.2421 0.0628
LJ 15 0.2184 0.7046
LJ 16 0.3164 0.6812
LJ 17 0.0000 0.0000
LJ 18 0.0000 0.0000
found:
56499 atoms
56559 bonds
9489 angles
23656 torsions
Error: pdb and rdparm disagree on number of atoms!
--
Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Tue May 19 2015 - 04:30:03 PDT
