Dera Tasneem, First thing to check is if you have read the -hbn or -hbm output upside down. This is a common mistake. Seriously.
Kind regards, Erik ______________________________ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 8 Feb 2017, at 06:06, Tasneem Kausar <tasneemkausa...@gmail.com<mailto:tasneemkausa...@gmail.com>> wrote: Dear all I am calculating hydrogen bond between protein and drug molecule using gmx hbond tool. I am using default value for hydrogen bond radius. Here is the command: gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm hbond.ndx I am selecting group 1 and 13. It shows many hydrogen bonds. Then I have calculated the percentage of hydrogen bond using perl script. There are there hydrogen bonds that show a significant existence. I wrote the snapshots of trajectories having all three hydrogen bonds. In every snapshot, when visulaized with a visulaization sofware such as chimera and LIGPLUS hydrogen bond of serin does not exist though it shows hydrophobic interaction with drug molecule. LIGPLUS gives a provision to show the missing hydrogen bond. When I have plotted by taking consideration serin hydrogen bond, it shows a bond length of 4.26 angstrom and like that in almost every extracted snapshot. In existence map serin is showing 92% abundance of hydrogen bond. This problem is occurring with serin only. Why is this happening? Is there a cut off problem with the visualization tools or something else? Is there an method to write the hydrogen bond and there distance simultaneously. Thanks in Advance Tasneem -- 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<mailto:gmx-users-requ...@gromacs.org>. -- 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.