Re: [gmx-users] g-hbond and N acceptors
David, Thanks for your reply. NH2 groups that are not aromatic (amines) one accept Hbonds of course. However there is not so much chemical knowledge in the program, and to make matters worse, you can not select acceptors or donors separately. Of course amine groups with a lone electron pair can in principle accept H-bonds. But in the case of proteins, no such groups are found (except on a deprotonated Lys). Peptide groups in the backbone as well as carboxyamide groups on Asn and Gln have hybrid orbitals which makes their structure planar and prevents to accept H-bonds. In proteins at reasonable pH, only deprotonated aromatic nitrogens on His should be considered acceptors. The GROMOS and HBPLUS manuals agree on this. In HBPLUS there is an option to accept other nitrogens as acceptors (see below) but only in cases where the protonation of His and orientation of Asn and Gln are not determined. These nitrogens are not considered acceptors by themselves. I would like to hack a correction for this in the code. I guess I would have to simply change line 400 of gmx_hbond.c (3.3.1) with something like : (*top-atoms.atomtype[i])[0] == 'NR5') Does this look right ? What is the difference between atomtype and atomtypeB ? Cheers, Michel FROM THE HBPLUS MANUAL Acceptors : 1. O (ie Main Chain COs of recognised amino - not imino - acid residues) 2. CYH SG, CSS SG, ASP OD1, ASP OD2, GLU OE1, GLU OE2, HIS ND1, MET SD, ASN OD1, GLN OE1, SER OG, THR OG1, TYR OH 3. Recognised acceptors of non-standard recognised molecules 4. Oxygen atoms in HETATM molecules (including waters) Atoms that may act as both donors and acceptors under the -X or -x options : 1. HIS CD2, HIS CE1, ASN OD1, ASN ND2, GLN OE1, GLN NE2 -x Exchange the side-chains of Histidine, Glutamine and Asparagnine. These side-chains are difficult to resolve crystallographically with certainty, which is why there is the option of adding potential hydrogen bonds that would be formed if HIS CD2 was actually ND1, HIS CE1 was NE2 and the nitrogens and oxygens of the ASN / GLN amide groups were actually the other way round. (Default is not to do this.) -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g-hbond and N acceptors
Hi, I'm studying protein-protein interaction, and have done extensive h- bond statistics. I'm still using g_hbond 3.1.4 for compatibility of the angle and distance criteria with older work (and there was at some point a segmentation fault problem with newer versions). Now looking at single occurences of h-bonds, I noticed some weird things : a series of NH2 -NH3 encounters between a GLN and a LYS reported as an h-bond, for example... Does the -nitacc option mean that _any_ nitrogen atom is automatically considered an acceptor ? Why would this surprising behavior be set by default ? Only nitrogens with a lone pair of electrons can be acceptors, such as the unprotonated one in histidines. Without the -nitacc option, does g_hbond completely neglect hbonds involving _any_ nitrogen acceptor ? Please tell me if I misunderstand something. Or has the behavior of g_hbond been modified in later versions of gromacs regarding the N- acceptor behavior ? Thanks, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g-hbond and N acceptors
Michel Cuendet wrote: Hi, I'm studying protein-protein interaction, and have done extensive h-bond statistics. I'm still using g_hbond 3.1.4 for compatibility of the angle and distance criteria with older work (and there was at some point a segmentation fault problem with newer versions). Now looking at single occurences of h-bonds, I noticed some weird things : a series of NH2 -NH3 encounters between a GLN and a LYS reported as an h-bond, for example... The new version has been tested by comparing to other programs and gives the same results. I am not sure what you are referring to. Does the -nitacc option mean that _any_ nitrogen atom is automatically considered an acceptor ? Why would this surprising behavior be set by default ? Only nitrogens with a lone pair of electrons can be acceptors, such as the unprotonated one in histidines. Without the -nitacc option, does g_hbond completely neglect hbonds involving _any_ nitrogen acceptor ? Please tell me if I misunderstand something. Or has the behavior of g_hbond been modified in later versions of gromacs regarding the N-acceptor behavior ? No, this is one of the few points that have not been altered. I guess you are correct that Hbonds are not expected for some of these interactions, like Gln - Lys. NH2 groups that are not aromatic (amines) one accept Hbonds of course. However there is not so much chemical knowledge in the program, and to make matters worse, you can not select acceptors or donors separately. Thanks, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
