I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the "bad for the health" sign. Btw, gromacs issues a lot of warnings, but not this one :D
What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. On Sat, Nov 26, 2011 at 3:55 PM, <chris.ne...@utoronto.ca> wrote: > There is rounding because of angstroms vs nanometers and both files > maintain 3 decimal places (see below). > > The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp > file. > > I see your point, but I don't think it matters. If you really need that > precision, then I'd think that you'd be using double precision gromacs > (which would still round the output .gro from pdb2gmx and not solve this > issue... just saying). > > gpc-f101n084-$ tail a.gro > 2GLY HA2 11 -0.426 0.215 0.193 > 2GLY C 12 -0.446 0.390 0.072 > 2GLY O 13 -0.368 0.440 -0.013 > 3NME N 14 -0.532 0.478 0.154 > 3NME H 15 -0.618 0.488 0.104 > 3NME CH3 16 -0.468 0.607 0.173 > 3NME HH31 17 -0.375 0.594 0.227 > 3NME HH32 18 -0.533 0.670 0.234 > 3NME HH33 19 -0.447 0.661 0.081 > 0.47330 0.80470 0.29640 > gpc-f101n084-$ tail a.pdb > ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 > ATOM 12 C GLY 2 -4.461 3.901 0.720 > ATOM 13 O GLY 2 -3.677 4.400 -0.128 > HETATM 14 N NME 3 -5.316 4.776 1.535 > HETATM 15 H NME 3 -6.182 4.876 1.044 > HETATM 16 CH3 NME 3 -4.685 6.072 1.731 > HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 > HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 > HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 > END > > -- original message -- > > There was no water. Version 4.5.5. Single precision. This is what I ran: > > pdb2gmx -f 1.pdb -p g1 -o g1 > grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top > mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene > Potential energy: 1.19780e+02 kJ/mol > > grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top > mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene > Potential energy: 1.15997e+02 kJ/mol > > The mdp file: > > integrator = md > nsteps = 0 > nstcomm = 1 > nstxout = 1 > nstvout = 1 > nstfout = 0 > nstlog = 1 > nstenergy = 1 > nstxtcout = 0 > nstlist = 0 > ns_type = simple > pbc = no > rlist = 0 > rcoulomb = 0 > rvdw = 0 > gen_vel = no > unconstrained-start = yes > lincs-warnangle = 30 > > The pdb file : > > HETATM 1 1HH3 ACE 1 -1.449 0.109 -0.581 > H > HETATM 2 CH3 ACE 1 -2.101 -0.268 0.202 > C > HETATM 3 2HH3 ACE 1 -1.708 0.090 1.151 > H > HETATM 4 3HH3 ACE 1 -2.109 -1.350 0.189 > H > HETATM 5 C ACE 1 -3.491 0.269 0.000 > C > HETATM 6 O ACE 1 -4.453 -0.401 -0.152 > O > ATOM 7 N GLY 2 -3.601 1.734 0.000 > N > ATOM 8 H GLY 2 -3.039 2.278 -0.623 > H > ATOM 9 CA GLY 2 -4.525 2.391 0.903 > C > ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 > H > ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 > H > ATOM 12 C GLY 2 -4.461 3.901 0.720 > C > ATOM 13 O GLY 2 -3.677 4.400 -0.128 > O > HETATM 14 N NME 3 -5.316 4.776 1.535 > N > HETATM 15 H NME 3 -6.182 4.876 1.044 > H > HETATM 16 CH3 NME 3 -4.685 6.072 1.731 > C > HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 > H > HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 > H > HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 > H > END > > > *In reply to chris.neale at utoronto.ca:* > > It's more useful if you provide more information. What was the .pdb > > file (can I download it from the pdb databank?) was there water? what > > version of gromacs? was it compiled in double or single precision? > > what were your mdp parameters? > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
