Thank you, Justin! I found the error message which was embedded in a lot of text. :P
As you said, the atom indexing is not a problem at all. The actual error is: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented When I changed ns_type to grid, the problem was solved! Thanks a lot! Peggy On Sat, Feb 14, 2009 at 4:26 PM, Justin A. Lemkul <[email protected]> wrote: > > > Peggy Yao wrote: > >> Unfortunately, no. :( When I tried to add ions to the system using: >> >> grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >> >> It return me an error without explanation: >> >> processing coordinates... >> double-checking input for internal consistency... >> >> There was 1 note >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.0.2 >> Source code file: grompp.c, line: 864 >> >> Fatal error: >> There were 1 error(s) processing your input >> ------------------------------------------------------- >> >> Did I make any mistake? I am new to MD simulation and Gromacs. The >> following are all the steps that I ran until the fatal error: >> >> > Probably. Search the entire output of grompp for the error message. I > don't remember grompp ever reporting a fatal error without printing the > actual problem somewhere that the user can see. > > If you can provide that information, as well as the contents of your .mdp, > there may be a chance to diagnose what's going on. As I said before, the > problem *shouldn't* be the number of atoms in the file. > > -Justin > > pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water >> spce >& pdb2gmx.log >> # add water >> editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log >> genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& >> genbox.log >> # add counter ions >> grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >& >> grompp_ion.log >> >> Peggy >> >> On Sat, Feb 14, 2009 at 3:31 PM, Mark Abraham >> <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> ----- Original Message ----- >> From: Peggy Yao <[email protected] <mailto:[email protected]>> >> Date: Sunday, February 15, 2009 10:24 am >> Subject: Re: [gmx-users] Atom index overflow after adding water >> To: [email protected] <mailto:[email protected]>, Discussion list for >> GROMACS users <[email protected] <mailto:[email protected]>> >> >> > Thank you, Justin! >> > >> > I changed the output files to .gro. >> > >> > pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o >> 1eia.gro -water spce >& pdb2gmx.log >> > # add water >> > editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log >> > >> genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& >> genbox.log >> > >> > However, the overflow error still occurs in the gro file: >> > >> > 32448SOL HW299996 9.410 8.282 1.575 >> > 32449SOL OW99997 9.923 8.813 0.726 >> > >> 32449SOL HW199998 9.874 8.726 0.735 >> > 32449SOL HW299999 9.900 8.856 0.639 >> > 32450SOL OW 0 0.018 7.452 0.502 >> > 32450SOL HW1 1 0.058 7.543 0.493 >> > 32450SOL HW2 2 -0.082 7.460 0.508 >> > >> 32451SOL OW 3 9.507 8.424 1.264 >> > 32451SOL HW1 4 9.596 8.379 1.250 >> > >> > What's wrong? Thanks a lot! >> >> Probably nothing. The issue is whether the parsing algorithm in >> grompp will handle the situation gracefully. Justin thinks it does. >> You should try it and see :-) >> >> Mark >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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