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 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 <[email protected]> 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 <[email protected]<mailto: >> [email protected]>> 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> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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