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?
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