AMBER Archive (2009)

Subject: Re: [AMBER] inpcrd and prmtop

From: FyD (
Date: Tue Mar 03 2009 - 04:19:43 CST

Dear "",

>> I have built a complex and saved the prmtop and inpcrd files with
>> water molecule, i forgot to save them in the gas phase, How to
>> obtain the inpcrd and prmtop for the same geometry without water
>> molecule.
> In principle you can directly modify the two files but maybe it is
> easiest to redo the procedure with leap after having removed the water
> coordinates. Best would be to always store your coordinates into a PDB
> file (command savepdb) which you should be able to easily load again in
> leap.

Yes, the best is to re-do the prmtop/prmcrd files...

That being said, you could play with the "rdparm" program and its
"stripwater" option (belongs to ptraj). You tell to the program that
you want to keep 0 water molecule, and you save the new
"" file (this does not work for ions I think).

Concerning the inpcrd file, you could convert the prmcrd file into PDB
file using ambpdb (ambpdb -aatm -p <
prmtop-withwater.crd > prmtop-withwater.pdb), then look when the
Cartesian coodinates (CC) of water molecules start in the PDB file,
compare the CC in the prmtop-withwater.crd & prmtop-withwater.pdb to
manually edit/remove the Water CC in the prmtop-withwater.crd files...

I hope this helps,
regards, Francois

AMBER mailing list