[gmx-users] Fwd: Drude in Gromac

[Justin Lemkul]

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

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

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