[gmx-users] Unable to generate file.gro with gromacs.4.6.3-1

[Mark Abraham]

Among other places, there was a thread here two days ago with that title
;-)
On Mar 23, 2014 3:34 AM, "Christopher Neale" <chris.neale at alum.utoronto.ca>
wrote:

> where do you learn this stuff ? ;)
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> Lemkul <jalemkul at vt.edu>
> Sent: 22 March 2014 21:50
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1
>
> On 3/22/14, 9:13 PM, Collins Nganou wrote:
> > Dear Users,
> >
> >   I am unable to generate the file.gro with  gromacs.4.6.3-1.
> > However, I have obtained the file.top after using
> >
> > pdb2gmx -f TTb.pdb -o TT.gro -p TT.top -ignh
> > ...
> >
> > This appears after I have change the version of gromacs from 4.5-4 to
> > 4.6.3-1
> > I am not able to find any error in the output.
> >
> > I will be very grateful the receive any suggestion...
> >
> > I wish you all a blessing weekend
> >
> >
> > Collins
> >
> >
> > My out put :
> >
> > Analyzing pdb file
> > Splitting chemical chains based on TER records or chain id changing.
> > There are 1 chains and 0 blocks of water and 4 residues with 37 atoms
> >
> >    chain  #res #atoms
> >    1 ' '     2     37
> >
> > All occupancies are one
> > Opening force field file
> > /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
> > Atomtype 1
> > Reading residue database... (amber99sb-ildn)
> > Opening force field file
> > /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
> > Residue 93
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
> > Residue 109
> > Sorting it all out...
> > Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
> > Residue 125
> > Sorting it all out...
> > Opening force field file
> > /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
> > Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
> > Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
> > Opening force field file
> > /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
> > Opening force field file
> > /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
> > Processing chain 1 (37 atoms, 2 residues)
> > Identified residue DT3 as a starting terminus.
> > Identified residue DT4 as a ending terminus.
> > 8 out of 8 lines of specbond.dat converted successfully
> > Opening force field file
> > /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
> > Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
> > Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
> > Checking for duplicate atoms....
> > Generating any missing hydrogen atoms and/or adding termini.
> > Now there are 2 residues with 63 atoms
> > Making bonds...
> > Number of bonds was 66, now 66
> > Generating angles, dihedrals and pairs...
> > Instruction non permise (core dumped)
> >
>
> An "illegal instruction" indicates that the binary was compiled for a
> different
> architecture, i.e. an incompatible GMX_CPU_ACCELERATION setting when
> compiling.
>   Did you copy the binaries over from another machine, or did you compile
> from
> source?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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