[gmx-users] How to ignore hydrogen of one part of a pdb file by pdb2gmx

[Justin Lemkul]

On 6/29/16 5:39 AM, 柯谱 wrote:
> Hello,
>
>             I have a pdb file that contains a transmembrane protein.  The
> protein needs to be treated by -ignh directive of pdb2gmx while the lipids do
> not(and can not, since there is no hdb file for lipids).  How can I process the
> structure without going through the insertion of the protein again?   Thanks!

Using -ignh is all or nothing; it cannot be selectively applied.  So either name 
the H in the protein appropriately or delete them yourself, before running pdb2gmx.

-Justin

-- 
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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

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