[gmx-users] Grompp not finding proper dihedral

[Justin Lemkul]

On 7/30/14, 2:59 AM, RINU KHATTRI wrote:
> check your topology file weather any coordinate is missing in your topology
> basically in angles region check your ffnonbonded.itp you have been pasted
> the line from lipid.itp or not
>

This issue is not related to coordinates or parameters from any lipid force field.

-Justin

>
>
> On Wed, Jul 30, 2014 at 12:15 AM, John Doe <helstreak at hotmail.com> wrote:
>
>> Hi,
>>
>> I'm attempting to simulate "polyethylene" using OPLS (I'm using Gromacs
>> 5.0.1-dev).  I'm using the files from:
>>
>> https://www.mail-archive.com/gmx-users@gromacs.org/msg19683.html
>>
>> I have moved the OPLS force field directory to my working directory and
>> placed "ffoplsaa.rtp" and "ffoplsaa.hdb" in the OPLS directory. I use
>> pdb2gmx (selecting the option for OPLS in my folder) to produce the gro and
>> top files
>>
>> """
>> gmx pdb2gmx -f polyethylene.pdb -o PE_processed.gro
>> """
>>
>> This works fine. I think enlarge the simulation box:
>>
>> """
>> gmx editconf -f PE_processed.gro -o PE_bigBox.gro -bt cubic -c -d 2.0
>> """
>>
>> Again, works fine.  I then move on to energy minimize using the mdp file
>> from:
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
>>
>> However, when I run grompp:
>>
>> gmx grompp -f minim.mdp -c PE_bigBox.gro -p topol.top -o PE_minim.tpr
>>
>> I get the following error:
>>
>> """
>> ERROR 1 [file topol.top, line 162]:
>>    No default Proper Dih. types
>>
>>
>> ERROR 2 [file topol.top, line 163]:
>>    No default Proper Dih. types
>>
>>
>> ERROR 3 [file topol.top, line 164]:
>>    No default Proper Dih. types
>>
>>
>> ERROR 4 [file topol.top, line 165]:
>>    No default Proper Dih. types
>>
>>
>> ERROR 5 [file topol.top, line 166]:
>>    No default Proper Dih. types
>> """
>>
>> I'm not quite sure why I'm getting this error because the dihedral are
>> defined in OPLS.  Take for instance ERROR 1.  This
>>   error correlates to the dihedral "HC-CT-CT-CT", however, in the OPLS
>> bonded parameters file, the dihedral is written out as "CT-CT-CT-HC", so
>>   I'm not sure why grompp is not processing this.  Does this dihedral
>> need to be reversed?  Then ERROR 2 corresponds to "CT-CT-CT-CT" which is
>> defined in the bonded parameters (file "ffbonded.itp").  So I'm not really
>> sure what's going on.
>>
>> Thanks for the help.
>> --
>> Gromacs Users mailing list
>>
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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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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