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! Peggy On Sat, Feb 14, 2009 at 2:40 PM, Justin A. Lemkul <[email protected]> wrote: > > > Peggy Yao wrote: > >> Dear all, >> >> Has anyone encountered the problem of atom index overflow in PDB files >> after adding water molecules? >> >> The following are what I did: >> >> pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.pdb -water >> spce >& pdb2gmx.log >> # add water >> editconf -bt cubic -f 1eia.pdb -o 1eia.pdb -c -d 0.9 >& editconf.log >> genbox -cp 1eia.pdb -cs spc216.gro -o 1eia_water.pdb -p 1eia.top >& >> genbox.log >> >> However, in 1eia_water.pdb, the atom index of the water section >> overflowed: >> >> ATOM 99996 HW2 SOL 2448 98.583 52.132 64.542 1.00 0.00 >> ATOM 99997 OW SOL 2449 1.182 45.201 68.242 1.00 0.00 >> ATOM 99998 HW1 SOL 2449 1.592 44.881 69.102 1.00 0.00 >> ATOM 99999 HW2 SOL 2449 0.222 44.931 68.212 1.00 0.00 >> ATOM 0 OW SOL 2450 93.503 42.681 67.002 1.00 0.00 >> ATOM 1 HW1 SOL 2450 94.353 42.351 66.592 1.00 0.00 >> ATOM 2 HW2 SOL 2450 93.633 42.831 67.982 1.00 0.00 >> ATOM 3 OW SOL 2451 94.993 42.441 73.082 1.00 0.00 >> >> How to solve this problem? >> >> > Well, the .pdb file format can only handle a fixed amount of digits when > numbering atoms. I don't know if using .gro format will be of any use, but > I routinely simulate systems of 200,000+ atoms with no problem, and any > index files I make are correctly numbered. > > -Justin > > Thanks, >> Peggy >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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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