[gmx-users] pdb2gmx response time

[Justin A. Lemkul]

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
> 

-- 
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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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