Yao Yao wrote:
Hi All,
when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got
stuck in the middle, showing
====================
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp
Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat
Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /share/apps/gromacs407/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /share/apps/gromacs407/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /share/apps/gromacs407/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /share/apps/gromacs407/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /share/apps/gromacs407/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Opening library file /share/apps/gromacs407/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 14 atoms
chain #res #atoms
1 '-' 1 14
No occupancies in AA.gro
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.atp
Atomtype 1
====================
Has anyone come across this before?
There are a variety of reasons this could be happening. You haven't provided
your command line or information about terminus selection, which could be
pertinent in the case of a single residue. Have you modified the .atp file in
any way? There was an old bug that might have affected this, but I can't
remember if it was specific to the 4.5.x series or not.
Otherwise, upgrade to version 4.5.4 and try again. Troubleshooting two-year-old
software is not terribly productive, especially when newer versions may have
resolved the issue.
-Justin
Thanks,
Yao
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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