[gmx-users] Umbrella pulling Drug + Ion channel
Andres Ortega Guerrero
og_andres15 at hotmail.com
Wed Mar 26 18:52:16 CET 2014
Thank you Justin ,
In my case i could get the geometries with this pull code, but,
mi pull_pbcatom0, is in the middle of the ion channel pore,
shouldn't i get positive and negatives distances ligand crossing this atom?
because i am getting distances as the center of the whole protein
or should i repeatthe pull code , and instead of protein, use 4 residues ( my channel has 4 chains)
in the middle of the pore?
Thank you Justin
> Date: Tue, 25 Mar 2014 12:32:24 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Umbrella pulling Drug + Ion channel
> On 3/25/14, 8:15 AM, Andres Ortega Guerrero wrote:
> > Yes during Equilibration, the drug and the channel was restraint, yesterday , i tried changing the pull_geometry to position
> > and it worked, i think that maybe there was problem with my cylinder configurations , this was my position configuration,
> > considering this, i might think that theres not a problem of stability could be this true?
> Likely something was wrong with the cylinder pull settings, yes. But if you
> accomplished what you needed with position, then I suspect it's not very
> worthwhile to dissect what that problem was.
> > thank you Justin in advance
> > ; Pull code
> > pull = umbrella
> > pull_geometry = position ;
> > pull_vec1 = 0.0 0.0 1.0 ;
> > pull_start = yes ; define initial COM distance > 0
> > pull_init1 = 0 0 0
> > pull_ngroups = 1
> > pull_group0 = Protein
> > pull_group1 = DOX
> > pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns
> > pull_k1 = 1000 ; kJ mol^-1 nm^-2
> > pull_pbcatom0 = 8485
> > Andrés
> 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
> 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.
More information about the gromacs.org_gmx-users