Dear justin please check this part of my .gro file. ... 630VAL C 6416 0.554 11.700 -0.442 630VAL O1 6417 0.522 11.605 -0.534 630VAL O2 6418 0.534 11.834 -0.454 631<1> N2 1 2.686 2.399 2.151 631<1> C20 2 2.613 2.375 2.230 631<1> C14 3 2.519 2.345 2.331 631<1> C10 4 2.464 2.452 2.405 ... I used the prodrg server and edited my protein.gro file. Is this correct? Where is my mistake? ُthanks in advanvce
On Tue, Dec 21, 2010 at 5:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > mohsen ramezanpour wrote: > >> Dear Justin >> >> WARNING 1 [file g-dist.mdp, line unknown]: >> Can only use nstype=Simple with pbc=no, setting nstype to Simple >> WARNING 2 [file complex.top, line 39718]: >> Bad box in file complex.gro >> >> Generated a cubic box 10.816 x 14.959 x 9.086 >> Warning: atom name 6439 in complex.top and complex.gro does not match (C18 >> - H9N) >> Warning: atom name 6440 in complex.top and complex.gro does not match (C6 >> - H9O) >> Warning: atom name 6441 in complex.top and complex.gro does not match (C11 >> - H19) >> Warning: atom name 6442 in complex.top and complex.gro does not match (H11 >> - C18) >> Warning: atom name 6443 in complex.top and complex.gro does not match (C15 >> - C6) >> Warning: atom name 6444 in complex.top and complex.gro does not match (H15 >> - C11) >> Warning: atom name 6445 in complex.top and complex.gro does not match (C17 >> - H11) >> Warning: atom name 6446 in complex.top and complex.gro does not match (F1 >> - C15) >> Warning: atom name 6447 in complex.top and complex.gro does not match (C16 >> - H15) >> Warning: atom name 6448 in complex.top and complex.gro does not match (H16 >> - C17) >> Warning: atom name 6449 in complex.top and complex.gro does not match (C12 >> - F1) >> Warning: atom name 6450 in complex.top and complex.gro does not match (H12 >> - C16) >> >> WARNING 3 [file complex.top, line 39718]: >> 12 non-matching atom names >> atom names from complex.top will be used >> atom names from complex.gro will be ignored >> > > These are very important warnings, and hence why I said one should never > blindly use -maxwarn unless you fully understand their implications. The > order of the contents of the coordinate file must match the order of the > moleculetypes listed in the [molecules] directive of the topology, and the > order of the underlying topologies must match. You've got a bunch of > mismatches here, indicating that at least one of these criteria is not > satisfied, so anything you do (be it simulation or analysis) will be > complete garbage. > > Fix your coordinate file and try again. Don't use -maxwarn. If grompp > fails, it's for a reason. > > -Justin > > >> besides I generated it as enzyme/drug tutorial. >> besides C12 is in line 2 from the end of the page. >> thanks in advance >> >> >> >> >> >> On Tue, Dec 21, 2010 at 5:11 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> mohsen ramezanpour wrote: >> >> Dear justin >> after using grompp without -maxwarn I faced these: >> >> NOTE 2 [file g-dist.mdp, line unknown]: >> You are using a plain Coulomb cut-off, which might produce >> artifacts. >> You might want to consider using PME electrostatics. >> >> >> This run will generate roughly 2 Mb of data >> writing run input file... >> >> There were 2 notes >> >> There were 3 warnings >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.0.7 >> Source code file: ../../../../src/gmxlib/gmx_fatal.c, line: 481 >> >> Fatal error: >> Too many warnings (3), grompp terminated. >> If you are sure all warnings are harmless, use the -maxwarn option. >> >> >> None of this output actually indicates what the errors are. I don't >> know if any of it will be relevant to the problem at hand, but >> without seeing what the errors are, there's no way to rule out >> incorrect input. >> >> >> besides it is in 6454 line of complex.gro >> >> >> How did you generate complex.gro? If it is line 6454, it is not >> numbered accordingly. That doesn't matter, in theory, but if you've >> just simply concatenated the protein and ligand coordinate files and >> left any extraneous information in the .gro file, it could be >> causing the error. >> >> -Justin >> >> >> >> >> >> >> On Tue, Dec 21, 2010 at 4:32 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> mohsen ramezanpour wrote: >> >> Dear All >> I did the Enzyme/drug tutorial and generated complex.gro and >> complex.top files as was said. >> Now I want to measure the distance between center of mass of >> protein and drug >> I used g_dist but I could not. >> I entered these commands(of course I made an index.ndx and >> g-dist.tpr): >> >> I used from an typical .mdp file to generate .tpr file by >> below >> command: >> >> grompp -c complex.gro -p complex.top -o >> g-dist.tpr -f g-dist.mdp -maxwarn 3 >> >> >> What warnings are you ignoring? This is, in general, a very >> bad idea. >> >> >> then, >> g_dist -f complex.gro -s g-dist.tpr -o >> g-dist.xvg >> >> but the result was an empty g-dist.xvg and: >> >> Fatal error: >> Unexpected end of file in file 631LIG C12 45 -0.475 >> -0.514 -0.434 at line 2 >> (Source file ../../../../src/gmxlib/confio. >> c, line 725) >> >> >> How many atoms are in complex.gro? To what line number does >> this >> atom entry correspond? It seems g_dist thinks the file >> should end >> here, prematurely. >> >> -Justin >> >> >> besides,I want to measure this distance befor erunning >> and as a >> vector. >> below is a part of my complex.gro: >> 631LIG F1 42 -0.701 -0.571 -0.151 >> 631LIG C16 43 -0.534 -0.501 -0.306 >> 631LIG H16 44 -0.491 -0.434 -0.232 >> 631LIG C12 45 -0.475 -0.514 -0.434 >> 631LIG H12 46 -0.394 -0.446 -0.459 >> >> >> thanks in advances >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> 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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> 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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 > 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 >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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