AMBER Archive (2003)

Subject: Re: MM_PBSA Errors

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Wed Feb 12 2003 - 03:50:23 CST

Hi Ramon,

First of all check the corresponding structure with the ambpdb program. The
syntax is:
ambpdb -p parm_top_file < snapshot.crd > snapshot.pdb

How it looks like?

You don't have to change NSTART and NSTOP. You can check the files
SUFFIX_C.all.out, SUFFIX_L.all.out and SUFFIX_R.all.out and check the total
energy until the 251 snapshot. It doesn't have to vary a lot.

I suppose your are calculating binding energies for inclusion complexes
host-guest. I used mm-pbsa for calculating binding energies for inclusion
complexes like guest-cyclodextrin. Sometimes I obtained this error and it was
usually due to a large distance between the guest and the host which means
that the guest wasn't still complexed by the host. Usually the msms program
can't calculate the energy for a such corresponding structure.

Hope it helps.
pascal

Ramón Garduño-Juárez wrote:

> Dear Amber users:
>
> I am using the AMBER tool known as MM_PBSA in order to perform a comparison
> between the energies between different orientations of some inclusion
> complexes. For some of them I have been able to run MM_PBSA to the end,
> thus obtaining the corresponding energies. However, for a few of them my
> run MM_PBSA crashes with the following error message:
>
> ERROR: MSMS program output is missing
> check snapshot # 251 in file
> try_GB_new_ibu.all.out
> correct and rerun mm_pbsa_statistics<in>out
>
> The snapshot number varies according to my sampling scheme
> The file try_GB_new_?????.out sometimes is that of the host, sometimes is
> that of the guest
>
> I have tried to get around this problem by increasing or decreasing NFREQ,
> NSTART or NSTOP parameters in the mm_pbsa script. My trajectory file comes
> from AMBER v5 and MM_PBSA comes from AMBER v6. As far as I can see mm_pbsa
> has worked in other cases but I wonder why I am getting this weird behavior
> and how I can fix it.
>
> I will appreciate any comments, hints and fixes. Much obliged.
>
> Ramón Garduño
> CENTRO DE CIENCIAS FISICAS
> UNIVERSIDAD NAL. AUTONOMA DE MEXICO 

--
***************************************************
 Dr. Pascal Bonnet
 School of Pharmacy and Pharmaceutical Sciences,
 University of Manchester, Oxford Road,
 Manchester, M13 9PL, U.K
 Tel:(+44) (0)161 275 2431
 http://www.man.ac.uk/~mbpsspb3