[gmx-users] Fwd: Drude in Gromac

[Christian Jorgensen]

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.






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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-- 
---------------------------
Christian Jorgensen
PhD student, King's College London
---------------------------