Hi Justin, I was thinking of doing that. I'll have to be careful about removing mass from the (correct) attached atoms to preserve the total mass of the system
----- Original Message ----- From: "Justin Lemkul" <[email protected]> To: [email protected] Sent: Thursday, April 23, 2015 2:39:20 PM Subject: Re: [gmx-users] Heavy Hydrogens On 4/23/15 4:25 PM, Matthew Harrigan wrote: > Hi all, > There is an option in pdb2gmx "-heavyh" which shuffles some mass from the > connected heavy atom to the hydrogen. I want to do this, but starting from a > top, gro pair of files. Specifically, I don't want gromacs to try to > regenerate all the forcefield parameters in my top file. Does anyone have > suggestions for how I can go about this? > Write a simple parser that modifies the listed masses in [atoms]. This should be straightforward in something like Perl or Python. -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 [email protected] | (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 [email protected]. -- 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 [email protected].
