AMBER Archive (2008)

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

From: Florian Haberl (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Wed Aug 13 2008 - 07:47:21 CDT

Hi,

On Wednesday, 13. August 2008, Hannes Wallnoefer wrote:
> 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
>
> :244-246,248-253,255-263,265-272,274-283,285-286,289-307,309-312,315-338,34
> :2-351,353-378,381-389,394-398,401,405-1968,1970-2366,2368-2853,2855-3165,3
> :167-3432,3434-3705,3707-4165,4167-5032,5034-5647,5649-99999
>
> trajout ./SNAPSHOTS_MOD/snapshot_com.crd.1
> trajout ./modified.pdb pdb
>
> greetings,
> Hannes
>

easist solution is to setup the system again without solvent, so if you use
something like (t,s)leap you only have to comment out the solvent and ion
lines.

>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu

greetings,

Florian 

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu