Thank you Justin for the tip. I have given .rtf file as input and the script has generated me the desired output .itp file. The command I used is as shown below.
./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf /usr/local/gromacs/share/gromacs/top/charmm36.ff Thank you very much Justin for the help. On Wed, Nov 5, 2014 at 6:05 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/5/14 7:33 AM, Venkat Reddy wrote: > >> Dear Justin, >> My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters >> available for cholesterol and oleate chain in POPC, I have clubbed both >> together to generate the topology for CO (rtf file). Now I want to convert >> this rtf to itp file. is there any shortcut to accomplish this task? >> >> > In theory, our conversion script should handle that, because all the .str > files are are .rtf and .prm entries, so if you don't have any new > parameters, it can probably convert the .rtf itself. Never tried it, but > you can probably make it work. Error messages are pretty descriptive in > case of any issues. > > -Justin > > > On Wed, Nov 5, 2014 at 5:57 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 11/5/14 7:03 AM, Venkat Reddy wrote: >>> >>> Thank you Joao for the quick reply. My system has single lipid molecule >>>> and >>>> I have pre- calculated charge information for every atom in the lipid. I >>>> have edited charges on individual atoms apart from atom types. >>>> By the way, Previous studies have reported a topology for same lipid but >>>> in >>>> NAMD convention. Is there any other tool to convert NAMD to GROMACS >>>> compatible format? >>>> >>>> >>>> You have to be careful here. I would not use CGenFF for lipids, but >>> for >>> reasons different than what Joao was saying. As is cautioned in the >>> CGenFF >>> description, you shouldn't use it for molecules for which a highly tuned >>> biomolecular force field already covers much of, if not all, of the >>> chemical space. The CHARMM36 lipid force field is highly optimized and >>> performs very well. CGenFF, by its nature, is generalized. With >>> generalization and increased transferability comes a decrease in >>> accuracy. >>> Coupling charges calculated by a different method (is it compatible with >>> what CHARMM normally requires, and are those charges tuned against the LJ >>> parameters of the atom types to give reasonable intermolecular and >>> water-water interactions?) with somewhat less accurate atom types and >>> bonded parameters will probably lead to a poor result because you've got >>> a >>> hodge-podge of a topology. >>> >>> What is this lipid that you're trying to parametrize? Are its functional >>> groups covered by the existing parameters in the CHARMM36 lipid force >>> field? If they are, you should absolutely be using those parameters >>> (charges, atom types, and bonded parameters). Even small inaccuracies or >>> imbalances can have a huge impact, especially on lipids, which are very >>> sensitive. >>> >>> -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]. >>> >>> >> >> >> > -- > ================================================== > > 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]. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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].
