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: 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]>wrote: > > > ----- 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 >
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