[gmx-users] to gro or not to gro

[chris.neale at utoronto.ca]

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?