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. besides it is in 6454 line of complex.gro On Tue, Dec 21, 2010 at 4:32 PM, Justin A. Lemkul <[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 | (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 >
-- 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
