[gmx-users] Charmm 36 parameter file for gromacs
phanvy120690 at gmail.com
Wed Aug 12 04:15:13 CEST 2015
Dear Dr. Justin and Gromacs User,
Thank you so much for your helps.
When I use charmm36 ff to generate the topology for lipid (DOPC). I got
many warning "Warning :Long bond "
And after get the topology, the total charge is very high (+888 e for DOPC
bilayer have 516 molecular). When I used grompp to generate the .tpr file,
I got the many error like this :
Error 3379 [file topol_Other_chain_D.itp, line 198252]
No defaut U-B types
Error 2379 [file topol_Other_chain_D.itp, line 98252]
No default Proper Dih.type
What can I do to modified the topology to get the correct charge and fix
the error ?
I download dopc.itp from Tieleman's website. I run simulation and all
things look fine. People have experiences, please tell me the difference
of this topology and the one on the charmm36 force field.
Thank you so much
2015-08-11 23:05 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:
> On 8/11/15 10:01 AM, Vy Phan wrote:
>> Dear Gromacs users,
>> On the .itp file on the charmm36 force field, I see the DOPC and other
>> lipid which have the [atom][bond] and [ impropers] parameter. I wonder
>> where is the parameter for [dihedrals].
> Angles and dihedrals are automatically generated from the bonded
> connectivity. Only mandatory directives are included in the .rtp entries.
> 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
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