AMBER Archive (2007)

Subject: Re: AMBER: Error- MM_PBSA calculation

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Thu Oct 11 2007 - 16:56:43 CDT

Vicky,

There are two possibilities here . . . 1) You have a bad mkcrd executable or
2) There are errors in the input file. To test the first, I would run
Example One from the MM-PBSA source directory in your AMBERHOME directory.
If that runs successfully, then you need to verify the path name and
integrity of the files you are trying to access (i.e. your md*.crd files).

Best of luck,

Scott

On 10/11/07, vikky 99 <vsaivikram_at_gmail.com> wrote:
>
> Dear Amber users,
>
> I am using MM_PBSA module in amber9 for calculating the Free binding
> energy of a complex (Protein + Inhibitor). At first i am generating
> snapshots for three systems, Complex, Receptor and ligand, from the entire
> trajectory. I managed to get the snapshots but all are empty when i tried to
> open them.
>
> Input:
> GENERAL
> PREFIX snapshot
> PATH ../
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ../_complex.top
> RECPT ../_receptor.top
> LIGPT ../_ligand.top
> GC 1
> AS 0
> DC 0
> MM 0
> GB 0
> PB 0
> MS 0
> NM 0
> @MAKECRD
> BOX YES
> NTOTAL 77135
> NSTART 1
> NSTOP 10
> NFREQ 1
> NUMBER_LIG_GROUPS 1
> LSTART 9487
> LSTOP 9546
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 9486
> @TRAJECTORY
> TRAJECTORY ../md1.crd
> TRAJECTORY ../md2.crd
> TRAJECTORY ../md3.crd
> @PROGRAMS
>
> Kindly some one suggests me how to solve it.
> Thanks in advance.
> Sai vikrama chaitanya. V
>

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