Hi Leila,
This is normal. I think there is a bond there to keep the H-O-H angle
correct as there are no lone pairs on the oxygen but not entirely sure.
Anyway, it is not a problem with conversion and occurs in every amber
prmtop.
Oliver
On 26 December 2010 11:24, leila karami <karami.leila1.gmail.com> wrote:
> Dear amber
> users
>
>
>
> merry
> christmas
>
>
>
> I did simulation in gromacs. I converted gromacs trajrctory file (xtc) to
> amber trajectory file (mdcrd) by VMD
> to do some analysis. I want to obtain .prmtop file. I have a pdb file
> containing protein and water (TIP3P model).
>
>
> in pdb file water molecules are as
> follows:
>
>
>
> ATOM 24068 O WAT 7487 57.300 0.280 45.070 1.00
> 0.00
> ATOM 24069 H1 WAT 7487 56.970 0.430 44.190 1.00
> 0.00
> ATOM 24070 H2 WAT 7487 58.180 0.660 45.060 1.00
> 0.00
> ATOM 24071 O WAT 7488 54.080 7.820 1.430 1.00
> 0.00
> ATOM 24072 H1 WAT 7488 53.930 6.900 1.180 1.00
> 0.00
> ATOM 24073 H2 WAT 7488 54.840 8.080 0.910 1.00
> 0.00
> ATOM 24074 O WAT 7489 50.570 51.250 54.030 1.00
> 0.00
> ATOM 24075 H1 WAT 7489 50.380 51.730 53.230 1.00
> 0.00
> ATOM 24076 H2 WAT 7489 51.410 50.820 53.870 1.00
> 0.00
>
>
> when I
> use
>
>
>
> com = loadpdb
> "com.pdb"
>
> saveamberparm com com.prmtop
> com.inpcrd
>
>
>
> -- ignoring the
> warnings.
>
>
>
> Building
> topology.
>
> Building atom
> parameters.
>
> Building bond
> parameters.
>
> Building angle
> parameters.
>
> Building proper torsion
> parameters.
>
> Building improper torsion
> parameters.
>
> total 359 improper torsions
> applied
>
> Building H-Bond
> parameters.
>
> Not Marking per-residue atom chain
> types.
>
> Marking per-residue atom chain
> types.
>
> (Residues lacking connect0/connect1
> -
>
> *these don't have chain types marked*:
>
>
>
> res total
> affected
>
>
>
> CGLY
> 1
>
> NGLY
> 1
>
> WAT
> 7406
>
>
> )
>
> (no
> restraints)
>
>
>
> when I load created .prmtop and converted .mdcrd files by VMD, there is
> problem only in water molecules.
>
>
> 1) the length of O-H bonds are longer than those of normal waters. 2) there
> are new bonds between H atoms
> of each water
> molecule.
>
>
>
> is this state normal? is it a visual program? Do trajectory file
> conversion
> done correctly? how to fix it?
> I need .prmtop file for some anlysis in
> ptraj.
>
> is there problem in .prmtop file? (meybe, it doesn't match with trajectory
> about waters)
>
> any help will highly apprecited.
>
>
>
>
>
>
>
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 26 2010 - 08:00:02 PST
