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

[Justin Lemkul]

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

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