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

[Christopher Neale]

If you want only the .gro file, then you don't need to run pdb2gmx. Try editconf -f my.pdb -o my.gro .

If your running pdb2gmx to get the .top file (the reason why pdb2gmx exists, although I agree that the program name is commonly confusing), then I can't help you much since that error message "Instruction non permise (core dumped)" does not seem to come from gromacs (based on a recursive grep of the 4.6.3 source code that I just ran).

Can you copy and paste commands to show that your pdb2gmx call works fine from gromacs 4.5.4 but not gromacs 4.6.3 ?

Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Collins Nganou <nganoucollins at gmail.com>
Sent: 22 March 2014 21:13
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1

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)
--
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