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

[Mark Abraham]

Hi,

Or separate your protein into its own .pdb file, run gmx pdb2gmx -f
justprotein.pdb -o renamed.pdb and manually re-combine the pdb files.

Mark

On Wed, Jun 29, 2016 at 12:04 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.