[gmx-users] PG/PE 3:1 lipid bilayer
Hello all, I got the pre equilibrated POPE/POPG 3:1 bilayer from http://www.softsimu.net/downloads.shtml While introducing the peptide to it found error with AtomTypes. I am using charmm36-mar2014.ff. How to solve this? Thanks in advance -- 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-requ...@gromacs.org.
Re: [gmx-users] CHARMM36 force field available for GROMACS
Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative entries in the residuetypes.dat, however we have not yet been able to add the covalent bonds necessary to reproduce the correct branched carbohydrate chains. Is there any solution for that? Roland seems to have one, although suboptimal. would it be possible to share it? Gianni -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM36-force-field-available-for-GROMACS-tp5011701p5015779.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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-requ...@gromacs.org.
Re: [gmx-users] CHARMM36 force field available for GROMACS
On 4/10/14, 2:51 AM, gsettanni wrote: Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative entries in the residuetypes.dat, however we have not yet been able to add the covalent bonds necessary to reproduce the correct branched carbohydrate chains. Is there any solution for that? Roland seems to have one, although suboptimal. would it be possible to share it? Using specbond.dat might help, but often these types of patches will require modification of atom types depending on the linkage, so there isn't any solution completely within pdb2gmx that will suffice, outside of building a residue from the original PRES entries in the CHARMM files, which is what it sounds like Roland's program does. -Justin -- == 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 jalem...@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-requ...@gromacs.org.
Re: [gmx-users] free energy caculation error
Hi Justin, thank you very much! according to your advise, my error is solved successfully. -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-caculation-error-tp5015758p5015783.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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-requ...@gromacs.org.
[gmx-users] the result of the free energy
Hi all, when i calculate the free energy of a molecule, the result is as the picture . i do not understand the true meaning. what is the relationship between dH/d(lambda) the .xvg file got and the free energy ? and what is the meaning of the lambda ? thank you in advance. -- View this message in context: http://gromacs.5086.x6.nabble.com/the-result-of-the-free-energy-tp5015784.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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-requ...@gromacs.org.
[gmx-users] (no subject)
-- New ideas, fragile as spring flowers, easily bruised by the tread of the multitude, may yet be cherished by the solitary wanderer., Fred Hoyle, *The Black Cloud*. Everybody knows that something can't be done until somebody turns up who doesn't know that it can't be done and he does it., Albert Einstein Sometime ago I met a fellow who was wearing an abnormally long tie - I mean, it was abnormally long because of how the knot had been made, not because the tie was an abnormally long one, and so I asked him why such an abnormally long tie, and you know what he told me? That the tie belonged to his grandfather!! -- 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-requ...@gromacs.org.
[gmx-users] the result of the free energy
Hi all, when i calculate the free energy of a molecule, the result is as the picture . i do not understand the true meaning. what is the relationship between dH/d(lambda) the .xvg file got and the free energy ? and what is the meaning of the lambda ? thank you in advance. http://gromacs.5086.x6.nabble.com/file/n5015785/Screenshot-2.png -- View this message in context: http://gromacs.5086.x6.nabble.com/the-result-of-the-free-energy-tp5015785.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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-requ...@gromacs.org.
Re: [gmx-users] the result of the free energy
On 4/10/14, 10:40 AM, jane wrote: Hi all, when i calculate the free energy of a molecule, the result is as the picture . i do not understand the true meaning. what is the relationship between dH/d(lambda) the .xvg file got and the free energy ? and what is the meaning of the lambda ? thank you in advance. http://gromacs.5086.x6.nabble.com/file/n5015785/Screenshot-2.png http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html -Justin -- == 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 jalem...@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-requ...@gromacs.org.
