AMBER Archive (2009)

Subject: Re: [AMBER] Problem with MM-PBSA energy calculation

From: Rubben Torella (rubben.torella_at_gmail.com)
Date: Tue May 26 2009 - 06:24:56 CDT

Hi Florent, thank you very much for your help. In fact the problem stands in
the generation of the snapshot or in the generation of the parmtop files...
now I am able to calculate the correct free energy of the protein.. when I
do the same calculation with the molecule, the structure is not correct...
all my molecules contain sulphur and I see the the only atoms that the
program builds not in the right way are the sulphur atoms.. do you know if
this element needs some particular treatment?
Thanks a lot for your previous advice.
Best regards
Rubben Torella

2009/5/25 Barbault Florent <florent.barbault_at_univ-paris-diderot.fr>

> Hello,
>
> I already had this message error from MMPBSA and the problem came from the
> prmtop files. One way to verify easily the snapshot generation is to create
> a pdb files of each of the three partners (com, rec and lig).
> ampbdb -p complex_without_wat.prmtop < com.crd.1 > test.pdb (you should do
> the same with the receptor and the ligand)
>
> Generally, if there is a problem a warning will appear. However, it could
> be useful to have a look of the structure with your favorite software...
>
>
> Hope it will help you,
> Regards
> Florent Barbault
>
>
>
> On Mon, 25 May 2009 17:58:41 +0200
> Rubben Torella <rubben.torella_at_gmail.com> wrote:
>
>> Hi Amber users,
>> I'm trying to calculate the binding free energy between a protein and a
>> molecule.
>> I have performed MD simulations, then I have picked the last snapshot from
>> the MD simulation, I have stripped the water molecules and the
>> counter-ions
>> from it as explained in the tutorial, and I have built the parmtop of the
>> ligand, receptor and complex, simply cutting from the pdb the coordinates
>> of
>> the atoms and then using xleap. Then I use the script in the example
>> folder
>> of mm_pbsa in order to create the snapshots of the complex, receptor and
>> ligand.
>> This script create the snapshot, I think correctly, but when I want to
>> calculate the free energy of binding using the script of binding in the
>> example folder, no output is created because of problem on the calculation
>> of the energy...
>> Here is my .log file errors:
>> WARNING: Missing BOND for MM in 0 -> Taken from -1
>> WARNING: Missing VDWNB for MM in 0 -> Taken from -1
>> I have this warning for every snapshot.. and finally no calculation has
>> been
>> done.
>> I don't know where is (are) my error (s)...
>> Thank you in advance for every answer...
>> Best regards
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences / Assistant professor
>
> NEW ADDRESS !!!
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://www.itodys.univ-paris7.fr/
> tel : (33) 01-57-27-88-50
> e-mail : florent.barbault_at_univ-paris-diderot.fr
> -------------------------------------------------
>
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