[gmx-users] Fwd: Drude in Gromac

[Justin Lemkul]

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 <jalemkul at 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
>>
>> jalemkul at 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

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

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