[gmx-users] TIP4 and pdb2gmx

[David van der Spoel]

On Wed, 2004-11-17 at 12:37 +0800, Frauke Meyer wrote:
> 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?
This is not necessary. The third hydrogen will replaced by a dummy and
its coordinates generated as soon as you do a simulation.
> 
> Frauke
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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