AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA !

From: Jiten (jiten_at_postech.ac.kr)
Date: Sun Jun 26 2005 - 19:43:13 CDT

Hai Pradipta,

Usually the mm_pbsa script works well of we modify correctly. From your
input file, I guess that you have two sequences of protein in your system as
yo utried to used NUMBER_REC_GROUPS 2 beforehand.

Did you used like this

NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 3129
RSTART 3130
RSTOP 3207

If you want to separate the two coordinate system, this will not be helpful.
Therefore, using one of the receptor group as the ligand will be more
meaningful like you have attempted.

In such case you need two more topology files for the two coordinate systems
apart from the complex.

#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./complex.top
RECPT ./recep1.top
LIGPT ./recep2.top

I guess there could be a bond between NGR 3130 3129 - did you check that -
I am not sure if we can separate the groups if they are bonded.

Best wishes,

Jiten
----- Original Message -----
From: "Pradipta Bandyopadhyay" <pradipta_at_iitg.ernet.in>
To: <amber_at_scripps.edu>
Sent: Sunday, June 26, 2005 9:43 PM
Subject: AMBER: MM_PBSA !

>
>
>
> I have one doubt about the mm_pbsa script. I am trying to generate the
> snapshots from my trajectory.
>
> The relevant part of my input file is:
> -----------------------
> BOX YES
> NTOTAL 28675
> NSTART 1
> NSTOP 5
> NFREQ 1
>
> NUMBER_LIG_GROUPS 1
> LSTART 3130
> LSTOP 3207
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 3129
> ----------------------------
> I am getting the following error message:
>
> Something wrong with NGR 3130 3129
>
> Actually in the AMBER directory
> $AMBERHOME/src/mm_pbsa/Examples/01GenerateSnapshots
> if I change mm_pbsa.in from NUMBER_REC_GROUPS 2 to 1
> and delete the last two RSTART and RSTOP, I get the same error
> message.
>
> Can anyone point out my mistake?
>
> regards,
>
> Pradipta
>
>
>
>
>
> -----------------------------------------------------------------------------------
> This email was sent from IIT Guwahati Webmail. If you are not the
> intended recipient, please contact the sender by email and delete all
> copies; your cooperation in this regard is appreciated.
> http://www.iitg.ernet.in
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu