Re: AMBER: ptraj: load crd without hydrogen (i.e. missing parm file)

From: Raik Grünberg <>
Date: Mon, 2 Aug 2004 11:30:56 +0200

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

> 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
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