[gmx-users] Fwd: Drude in Gromac

[Christian Jorgensen]

Hello,
I downloaded and compiled the Gromacs v5 with drude clone


git clone git://git.gromacs.org/gromacs.git cd gromacs git checkout drude



I'm trying to run

$GRMHOME/gmx pdb2gmx -f sf.pdb -o sf.gro -ff drude-2013b_3may2016 -ter <
input



I get the following run:


All occupancies are one

Opening force field file ./drude-2013b_3may2016.ff/atomtypes.atp

Atomtype 137

Reading residue database... (drude-2013b_3may2016)

Opening force field file ./drude-2013b_3may2016.ff/aminoacids.rtp

Detected a non-polarizable force field

Residue 65

Sorting it all out...

Opening force field file ./drude-2013b_3may2016.ff/dna.rtp

Detected a non-polarizable force field

Residue 73

Sorting it all out...

Opening force field file ./drude-2013b_3may2016.ff/aminoacids.hdb

Opening force field file ./drude-2013b_3may2016.ff/dna.hdb

Opening force field file ./drude-2013b_3may2016.ff/aminoacids.n.tdb


-------------------------------------------------------

Program:     gmx pdb2gmx, version 2016-dev-20160902-dc92704

Source file: src/gromacs/gmxpreprocess/ter_db.cpp (line 147)


Fatal error:

Reading Termini Database: expected 3 or 4 items of atom data instead of 5 on

line

  N ND3P3A 13.6070  1.62807 -1 0.001298 0.8950


For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------

./run.sh: line 14: 83898 Abort trap: 6           $GRMHOME/gmx pdb2gmx -f
sf.pdb -o sf.gro -ff drude-2013b_3may2016 -ter < input


What can I do?
Chris