[gmx-users] pdb2gmx ffG43a1 force field

[Justin Lemkul]

On 10/16/14 10:55 PM, Nilesh Dhumal wrote:
> Hello,
>
> I am generating .top file using pdb2gmx and choose ffG43a1 force field
> from the list.
>
> pdb2gmx is running for an hour. Here I pasted the last part appeared on
> screen
>
> Select the Force Field:
>   0: GROMOS96 43a1 force field
>   1: GROMOS96 43a2 force field (improved alkane dihedrals)
>   2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>   3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>   4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>   5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>   6: [DEPRECATED] Gromacs force field (see manual)
>   7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>   8: Encad all-atom force field, using scaled-down vacuum charges
>   9: Encad all-atom force field, using full solvent charges
> 0
> Opening library file /usr/share/gromacs/top/ffG43a1.rtp
> Opening library file /usr/share/gromacs/top/aminoacids.dat
> Opening library file /usr/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 /usr/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 /usr/share/gromacs/top/vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /usr/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file /usr/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /usr/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading cu.gro...
> Read 'Title', 156 atoms
> Opening library file /usr/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 156 atoms
>
>    chain  #res #atoms
>    1 '-'     1    156
>
> No occupancies in cu.gro
> Opening library file /usr/share/gromacs/top/ffG43a1.atp
> Atomtype 1
> Cu
>
>
> Could any one tell why is it taking so long time.
>
> Total number of atom are 156 in system.
>

And they're all in one residue - what is in the coordinate file?  There's no 
reason for pdb2gmx to run that long; it's clearly stuck on something bizarre in 
your input file that it can't resolve.  Have you modified the force field in any 
way?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================