OK, I'll answer this one myself...
On Thursday 29 July 2004 12:34, Raik Grünberg wrote:
> I would like to load a trajectory intro ptraj from which I already stripped
> off the hydrogens, removed some residues etc. I.e. what I have is a crd
> file and a PDB file of exactly same content. What I DON'T have is a parm
> file for the modified PDB/Crd.
> Solutions I could think of are:
> A) convince tleap to create a parm from the PDB without completing residues
I didn't find a way of doing that.
> B) create a standard parm with hydrogens but convince ptraj to not expect
> any of them
didn't work either.
But this strategy seems to work:
1) first tleap run:
p = loadPdb noH.pdb
saveAmberParm p temp.parm temp.crd
2) create PDB from temp.parm, temp.crd:
ampdb -p temp.parm < temp.crd > temp.pdb
3) identify all atoms that are in temp.pdb but not in noH.pdb and generate a
second tleap script
...some involved python code...
4) second tleap run:
p = loadPdb temp.pdb
remove p.1 p.1.12
remove p.1 p.1.14
...
saveAmberParm p noH.parm noH.crd
The resulting parm file can be used to load the trajectory w/o hydrogens into
ptraj.
Raik
>
> For A) I could do 2 tleap cycles - first creating standard parm / crd files
> from the modified PDB, then identifying which atoms have been added by leap
> and run tleap again, this time deleting all these atoms with "delete
> <unit.resnr.atom_name>". Could that work??
> Is there an easier solution?
>
>
> Many thanks for any advise!
> Raik
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Received on Mon Aug 02 2004 - 10:53:00 PDT
