On 9/16/16 10:58 AM, Christian Jorgensen wrote:
Thank you, I will do so.
I was adding the 1 in drude-2013b_3may2016.ff/aminoacids.rtp


[ bondedtypes ]

; Col 1: Type of bond

; Col 2: Type of angles

; Col 3: Type of proper dihedrals

; Col 4: Type of improper dihedrals

; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.

; Col 6: Number of excluded neighbors for nonbonded interactions

; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1

; Col 8: Remove propers over the same bond as an improper if it is 1

; Col 9 Added to read polarizable

; bonds  angles  dihedrals      impropers all_dihedrals nrexcl HH14
RemoveDih

          1              5                      9                2
      1                       3              1         0  1   1


I get the idea, maybe I'm just dumb but it didn't work for me.


Well, what you've shown there has 10 columns instead of 9, so that should trigger a different error.

I updated the files on our website if you want to try from a clean force field.

If you have any other problems, contact me directly and we can work on it offline. This isn't an official feature yet (due to the remaining DD bug I haven't gotten this merged into the master repo yet).

-Justin






On Fri, Sep 16, 2016 at 3:36 PM, Justin Lemkul <jalem...@vt.edu> wrote:



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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--
==================================================

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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