[gmx-users] CHARMM27 hates my DMPC

[Justin Lemkul]

On 4/4/17 9:39 AM, Vytautas Rakeviius wrote:
> Thanks, I reused DMPC layers from CHARMM-GUI after some editing.
> I was able to pin-down issue here, test file:
> http://www.mediafire.com/file/usuv55c3j505ec2/test.pdb
> I can do: <http://www.mediafire.com/file/usuv55c3j505ec2/test.pdb>
> gmx pdb2gmx -f test.pdb -o test.gro -water spce
> <http://www.mediafire.com/file/usuv55c3j505ec2/test.pdb>
> Without error. But if I do: <http://www.mediafire.com/file/usuv55c3j505ec2/test.pdb>
> gmx pdb2gmx -f test.pdb -o test.gro -water spce -ignh
> I get error about hydrogen which I try to ignore. Very strange for me. -ignh
> option is not possible with CHARMM ff?
>
>

Sure it is, but only when applied properly.

-ignh tells pdb2gmx to ignore H atoms and try to rebuild them.  If you haven't 
constructed a suitable .hdb entry for your residue, you're just going to cause 
errors for yourself because now you've ignored atoms, which are considered missing.

-Justin

>
>
> On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:
>> Hello,
>> I have my system with DMPC bilayers in pdb and try to convert it into GROMACS
> input. Because system is with lipids I think chose CHARMM27 ff. But still I get
> lots of warnings like that:
>>
>> https://pastebin.com/K8dHKkUi
>> Also I add my DMPC pdb as example. What should I do? Rename all my DMPC
> atoms?Thanks for all suggestions.
>
>>
>>
>
> This is the same with any force field; the atom names have to match the force
> field's expectations.
>
> If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI.
> It's guaranteed to have CHARMM-compliant nomenclature (and you should be using
> CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as
> good for lipids).
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

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

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

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