AMBER Archive (2009)

Subject: Re: [AMBER] MM-PBSA problem

From: Giorgos Lamprinidis (lamprinidis_at_pharm.uoa.gr)
Date: Mon Jul 06 2009 - 03:07:14 CDT

Dear Rubben,

I am using a receptor having one crystallographic water molecule. The water
molecule was placed, by mistake, at the end of the file (instead for the
ligand) so the numbering for the ligand were all wrong. So I have to
re-create the solvated files (having the correct order rec, water, ligand),
and re-run the job .

Thanks again
George

----- Original Message -----
From: "Rubben Torella" <rubben.torella_at_gmail.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Friday, July 03, 2009 4:57 PM
Subject: Re: [AMBER] MM-PBSA problem

> 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
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber