AMBER Archive (2009)

Subject: Re: [AMBER] MM-PBSA problem

From: Rubben Torella (rubben.torella_at_gmail.com)
Date: Fri Jul 03 2009 - 08:57:09 CDT

Hi George.
Try to check the ligand structure with ambpdb in the folder SNAPSHOT...
check if the structure is right (i think not beacuse i had the same
problem...). If this is the error, check if the correct number of atoms in
the input file is right...
I hope these informations help you ...

2009/7/3 Giorgos Lamprinidis <lamprinidis_at_pharm.uoa.gr>

> Dear all,
>
>
>
> I am trying to run a MM-PBSA simulation (receptor + ligand). I prepared the
> ligand using the
>
> "BASIC WORKSHOP HANDS ON TUTORIAL 4" to calculate partial charges and
> missing parameters. Then i prepared the jobs using the Advanced Tutorial A3.
> I run the jobs without problem. When i run the binding_energy.mmpbsa script,
> the output results shows something very strange. The numbers for complex and
> receptor were fine, but for the ligand i got extremely big numbers as shown
> in the attached files. Can someone imagine why this happened? Has anyone
> else had the same problem? Please tell me which other files I must attached
> to help you find a solution.
>
>
>
> Best Regards,
>
>
>
> Dr George Lamprinidis
>
> School of Pharmacy
>
> University of Athens
>
> Greece
>
>
>
>
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