On 9/16/16 10:29 AM, Christian Jorgensen wrote:
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?

I need to update the force field files. I removed the -charmmdrude flag (because it was confusing) and subsequently changed the .rtp file format to automatically detect polarizable force fields.

In the meantime, add an additional 1 in the [bondedtypes] of the .rtp files to trigger polarizable force field reading.

Caveat: there is a lingering bug in the DD implementation that causes random failures. I do not have the fix finished, so running with OpenMP is the only thing I can guarantee works at the moment.

I will upload new force field files to our website sometime soon.

-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

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

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