AMBER Archive (2008)

Subject: Re: AMBER: modified parmtop file from ptraj?

From: Thomas Cheatham (
Date: Wed Aug 13 2008 - 12:43:24 CDT

> Is it possible to get a parmtop file out of ptraj after modifying the structure?
> I stripped water molecules from a single snapshot in ptraj and need a modified
> parmtop for mm_pbsa. I tried to save the modified structure as pdb-file and
> generate a new parmtop with leap, but when i try to use that new parmtop with
> the modified coordinate file saved from ptraj it doesn't work. For instance the
> ambpdb command says:

> Here is my ptraj input:
> trajin ./SNAPSHOTS/snapshot_com.crd.1
> strip :Cl-
> strip
> :244-246,248-253,255-263,265-272,274-283,285-286,289-307,309-312,315-338,342-351,353-378,381-389,394-398,401,405-1968,1970-2366,2368-2853,2855-3165,3167-3432,3434-3705,3707-4165,4167-5032,5034-5647,5649-99999
> trajout ./SNAPSHOTS_MOD/snapshot_com.crd.1
> trajout ./modified.pdb pdb

Only one trajout command is processed; also, if you want it in a format
suitable for ambpdb, you need to output as a restrt

trajout ./SNAPSHOTS_MOD/snapshot_com.crd.1 restrt

The PDB should work however, although you will have to use the "setBox"
command to add box information.

-- tec3
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