AMBER Archive (2008)

Subject: AMBER: modified parmtop file from ptraj?

From: Hannes Wallnoefer (Hannes.Wallnoefer_at_uibk.ac.at)
Date: Wed Aug 13 2008 - 07:14:34 CDT

Hi amber-users,

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:

Image PC Routine Line Source
ambpdb 080BE3C3 Unknown Unknown Unknown
ambpdb 080BD9E3 Unknown Unknown Unknown
ambpdb 0808934A Unknown Unknown Unknown
ambpdb 08062946 Unknown Unknown Unknown
ambpdb 080625E1 Unknown Unknown Unknown
ambpdb 080759FD Unknown Unknown Unknown
ambpdb 08073606 Unknown Unknown Unknown
ambpdb 0804CEAA Unknown Unknown Unknown
ambpdb 0804A6CE Unknown Unknown Unknown
ambpdb 08049DB1 Unknown Unknown Unknown
libc.so.6 B7CD9FE0 Unknown Unknown Unknown
ambpdb 08049D11 Unknown Unknown Unknown

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

greetings,
Hannes

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