Re: [gmx-users] How does x2top recognize between alkane C and alkene C
On 7/16/15 12:47 AM, sridhar dwadasi wrote: Thank you for the response. In case of an all atom representation, the connections are different. What about a united atom representation? The g_x2top supports Gromacs 53a5 forcefield right? If you write an .n2t file for it, sure. Can we get a topology with x2top only for an all atom representation? Or is there anyway to get it for gromos or opls ua ? No, it works with any force field for which an .n2t file exists. -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 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] How does x2top recognize between alkane C and alkene C
Hi Dr. Justin Lemkul, Thank you for responding again. I'm still not understanding it :(. I'll try to be more clear. Taking the example of OPLS UA, we have different atom types for united alkene atoms (-CH= and CH2=) and alkanes (-CH2-). When I represent the connections in n2t file, the -CH2- and -CH= will have two connections each. and the distances with other united carbons are 0.154nm and 0.140 nm as I have mentioned before. I have been giving the same information in the .n2t file. Based on the order in which they appear in the .n2t file, the atom appearing first is being taken by x2top to create the topology. I hope I made my problem clear. I'm unable to post my .n2t file now as I do not have it with me at the moment. If required I can post it tomorrow. Thanks and Regards Sridhar -- 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] How does x2top recognize between alkane C and alkene C
On 7/16/15 12:57 PM, sridhar dwadasi wrote: Hi Dr. Justin Lemkul, Thank you for responding again. I'm still not understanding it :(. I'll try to be more clear. Taking the example of OPLS UA, we have different atom types for united alkene atoms (-CH= and CH2=) and alkanes (-CH2-). When I represent the connections in n2t file, the -CH2- and -CH= will have two connections each. and the distances with other united carbons are 0.154nm and 0.140 nm as I have mentioned before. I have been giving the same information in the .n2t file. Based on the order in which they appear in the .n2t file, the atom appearing first is being taken by x2top to create the topology. I hope I made my problem clear. I'm unable to post my .n2t file now as I do not have it with me at the moment. If required I can post it tomorrow. Yes, please post the .n2t file. Just keep in mind that x2top is a very simplistic program; you may have to play some tricks to get such a subtle distinction to work correctly. UA models will be particularly tricky because there won't necessarily be any H to distinguish different forms. You may have to either play with the specified bond length (putting one outside of the 10% tolerance of the other) or re-compile the code after modifying the allowable tolerance. In this case, 10% may be too permissive. -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 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.
[gmx-users] How does x2top recognize between alkane C and alkene C
Thank you for the response. In case of an all atom representation, the connections are different. What about a united atom representation? The g_x2top supports Gromacs 53a5 forcefield right? Can we get a topology with x2top only for an all atom representation? Or is there anyway to get it for gromos or opls ua ? Thanks and Regards Sridhar -- 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] How does x2top recognize between alkane C and alkene C
On 7/13/15 1:38 AM, sridhar dwadasi wrote: Dear gromac users, I'm using g_x2top (4.6.7 version), to generate a topology. The compound contains double bonds. I have a problem in setting correct topology. The C1 in both the cases -C1H=C2H2 and -C1H2- is being assigned the same type, though I'm mentioning different distances in the n2t file. This may be due to the small difference in distance (0.140 nm and 0.154 nm). Can anyone suggest a way to go about this? Because 0.14 and 0.154 are exactly 10% apart (w.r.t. 0.140) so x2top can't distinguish between them based solely on bond length. The bonded connectivity is different, though, in terms of C1 (bonded to 3 groups only) so that suggests your .n2t file isn't constructed correctly. C1 in the alkane should have 4 substitutents, two of which are H. In the alkene, 3 substituents, with 1 H. -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 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.
[gmx-users] How does x2top recognize between alkane C and alkene C
Dear gromac users, I'm using g_x2top (4.6.7 version), to generate a topology. The compound contains double bonds. I have a problem in setting correct topology. The C1 in both the cases -C1H=C2H2 and -C1H2- is being assigned the same type, though I'm mentioning different distances in the n2t file. This may be due to the small difference in distance (0.140 nm and 0.154 nm). Can anyone suggest a way to go about this? Thanks and Regards Sridhar -- 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.
