AMBER Archive (2008)

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

From: Daniel Cappel (daniel.cappel_at_uni-wuerzburg.de)
Date: Wed Aug 13 2008 - 08:37:19 CDT

Hi Hannes,

rdparm can generate modified parmtop files. You can read in the original
file, e.g. strip water like with ptraj and finally write a new parmtop file.

Regards
Daniel

Hannes Wallnoefer schrieb:
> 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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