[gmx-users] TIP4 and pdb2gmx

[Frauke Meyer]

Hi,

can I generate TIP4 waters with pdb2gmx starting from coordinates for
the water oxygens?

pdb2gmx -f 1.pdb -o out.pdb

gives:

Now there are 1 residues with 4 atoms
Making bonds...
Warning: Short Bond (1-4 = 0 nm)
Opening library file
/home/fmeyer/prog/bin/gmx321/share/top/aminoacids.dat
Number of bonds was 3, now 3
Generating angles, dihedrals and pairs...
There are    0 dihedrals,    0 impropers,    3 angles
             0 pairs,        3 bonds and     0 dummies
Total mass 18.015 a.m.u.
Total charge 0.000 e
Writing topology

with 1.pdb:
ATOM   5663  OW  HO4   917      20.906  68.286   4.613  1.00  0.00

and out.pdb:
ATOM      1  OW  HO4     1      20.906  68.286   4.613  1.00  0.00
ATOM      2  HW1 HO4     1      21.722  68.286   5.190  1.00  0.00
ATOM      3  HW2 HO4     1      20.090  68.286   5.190  1.00  0.00
ATOM      4  HW3 HO4     1      20.906  68.286   4.613  1.00  0.00

OW and HW3 are at the same position - how to tell pdb2gmx to generate a
bond as specified in ffoplsaabon.itp?

Frauke