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? I do notice that FDp is between HOH and SOL but if I remove FDP, my ligand will be removed. 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. Please, could help me with both my problems. On Fri, Aug 10, 2012 at 6:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/10/12 1:05 PM, Ankita naithani wrote: >> >> Dear All, >> >> I have been trying to perform simulation for a Protein and Ligand >> complex. However, when I run genion, I get an error "The solvent group >> SOL is not continuous: index[37530=23341, index[3754]=23606. >> >> I remember reading someone posting a similar problem and the solution >> was provided, according to which we need to manipulate the co-ordinate >> file and topology file. But, the problem is I really cannot understand >> at the moment as to what exactly changes I should make in order to run >> it and rectify this error. I would be really grateful if someone >> could help me and let me know as to what exactly and how I need to >> incorporate the changes. Also, the co-ordinate file, should the >> changes be made to the one obtained after running the genbox step? >> > > In the coordinate file, you'll find lines for SOL, then something else, then > more SOL. Your SOL lines need to be continuous, so you have to cut out > whatever is breaking the two solvent blocks, put it either before or after > SOL, and then make sure the [molecules] section of the topology agrees with > contents of the new coordinate file in terms of number of molecules and > order of appearance. > > -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. 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