Hi Justin, Thank you so much for your reply. It really helped me a lot.
I think I have managed to clear this step. Thanks once again. Best Wishes, On Fri, Aug 10, 2012 at 6:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/10/12 1:26 PM, Ankita naithani wrote: >> >> Hi Justin, >> >> Thank you for your response. >> >> The co-ordinate file that you have mentioned. Is it the one obtained >> after running pdb2gmx step or the one after running genbox step? >> >> Also, I am putting few outputs for your referral.. >> >> My co-ordinate file after building topology and incorporating my >> ligand topology, looks like this: >> >> ---- >> 498GLU O119587 0.147 1.260 4.509 >> 498GLU O219588 0.017 1.177 4.669 >> 501HOH OW19589 -3.995 3.677 -0.161 >> ---- >> 2139HOH HW223341 0.013 0.653 1.232 >> 1FDP O1P 1 -0.608 6.909 -0.874 >> 1FDP P1 2 -0.474 6.859 -0.904 >> ----- >> 1FDP O4P 23 0.758 0.467 2.079 >> 1ATP O1G 1 -3.672 4.724 -0.730 >> 1ATP PG 2 -3.697 4.678 -0.871 >> ------- >> 1ATP H62 36 3.986 0.936 1.930 >> 1ATP H61 37 4.112 0.822 1.964 >> 1OXL O1 1 -3.442 4.377 -0.541 >> 1OXL C1 2 -3.431 4.424 -0.655 >> >> My co-ordinate file after defining box looks like this: >> >> 498GLU C19586 12.309 9.794 8.852 >> 498GLU O119587 12.411 9.858 8.823 >> 498GLU O219588 12.281 9.775 8.983 >> 501HOH OW19589 8.269 12.275 4.153 >> 501HOH HW119590 8.351 12.275 4.210 >> 501HOH HW219591 8.187 12.275 4.210 >> 503HOH OW19592 10.623 12.907 4.675 >> ---------------- >> 2139HOH HW123340 12.195 9.170 5.661 >> 2139HOH HW223341 12.277 9.251 5.546 >> 1FDP O1P23342 11.656 15.507 3.440 >> 1FDP P123343 11.790 15.457 3.410 >> 1FDP O2P23344 11.857 15.521 3.280 >> >> >> My co-ordinate file after solvation looks like this: >> >> 498GLU OE219585 11.824 9.468 8.693 >> 498GLU C19586 12.309 9.794 8.852 >> 498GLU O119587 12.411 9.858 8.823 >> 498GLU O219588 12.281 9.775 8.983 >> 501HOH OW19589 8.269 12.275 4.153 >> 501HOH HW119590 8.351 12.275 4.210 >> ---------- >> 2139HOH HW223341 12.277 9.251 5.546 >> 1FDP O1P23342 11.656 15.507 3.440 >> 1FDP P123343 11.790 15.457 3.410 >> ------------ >> >> 1FDP O423604 15.520 10.331 5.622 >> 1FDP O223605 15.614 10.234 5.451 >> 2SOL OW23606 0.230 0.628 0.113 >> 2SOL HW123607 0.137 0.626 0.150 >> 2SOL HW223608 0.231 0.589 0.021 >> 3SOL OW23609 0.569 1.275 1.165 >> 3SOL HW123610 0.476 1.268 1.128 >> 3SOL HW223611 0.580 1.364 1.209 >> 4SOL OW23612 1.555 1.511 0.703 >> ------------- >> >> 91503SOL HW198110 16.284 14.907 11.256 >> 91503SOL HW298111 16.159 14.910 11.360 >> 91504SOL OW98112 14.935 15.974 11.472 >> 91504SOL HW198113 15.034 15.963 11.463 >> 91504SOL HW298114 14.895 15.888 11.504 >> >> ---------------------------------- >> >> and my topology file has following: >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> Protein_chain_B 1 >> Protein_chain_C 1 >> Protein_chain_D 1 >> SOL 167 >> SOL 379 >> SOL 305 >> SOL 400 >> FDP 4 >> ATP 4 >> OXL 4 >> SOL 91503 >> >> >> I think you are talking about the co-ordinate file obtained after >> solvation, right? >> > > Yes. > > >> I do notice that FDp is between HOH and SOL but if I remove FDP, my >> ligand will be removed. >> > > I didn't say to remove it, I said to change its position within the > coordinate file. Right now, you have FDP, ATP, and OXL breaking up your SOL > section. You can't do that - all the SOL entries need to be continuous in > the coordinate and topology files. > > >> The second thing I noticed is that I had put the information for all >> the three ligands i.e. FDP,ATP and OXL but subsequently, I find that >> only FDP is present in these files and not ATP and OXL. >> > > Then you need to figure out at which point they got deleted and re-add them, > otherwise you'll have plenty of more problems later on. > > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ankita Naithani -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists