----- Original Message ----- From: Peggy Yao <[email protected]> Date: Sunday, February 15, 2009 10:24 am Subject: Re: [gmx-users] Atom index overflow after adding water To: [email protected], Discussion list for GROMACS users <[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] 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
