Dear Ben,
I think that my problem is due to the parametrization of the compound, I tried to parametrize the compound herein reported, using antechamber and leap. At the end just two kind of dihedrals were missing:
the ca-ca-ce-ca, and the c2-ce-ca-ca dihedrals. For the ca-ca-ce-ca dihedrals I used the following parameters:
N=2
PK/IDIVF=3.2500
Po=Pi
description=1.2000
whilst for the c2-ce-ca-ca dihedral I used, this ones:
N=2
PK/IDIVF=6.6500
Po=Pi
description=1.2000
I also checked for steric clash, but I didn't find it, the system is very small a water box of 15 A, the compound and 1 CL-.
I think that the parameters used are not the best one…. any suggestions?
thank you very much,
Agostino
Il giorno 28/mar/2012, alle ore 22:22, Ben Roberts ha scritto:
> Hi Agostino,
>
> On 29/03/2012, at 4:33 AM, Agostino Bruno wrote:
>
>> Dear all,
>>
>> I am writing you because I tried to parametrize a ligand using xleap. I
>> parametrized a ligand in a TIP3PBOX with 1 Cl- atom (so as to neutralize the
>> net charge). During the parametrization stage everything seems work well. At
>> the end I obtained the ligand.prmtop, ligand.inpcrd, and ligand.pdb files.
>> First of all I checked the generated fiels using vmd, and everything seems ok.
>> After that I tried to minimize the ligand using Amber11, I used one processor
>> and the command line:
>>
>> sander -i minimization.in -o minimization.out -p prova.prmtop -c prova.inpcrd
>> -ref prova.inpcrd -r mini_restrt.
>>
>> But Amber almost immediately crashed with this error message:
>>
>> Segmentation fault.
>
> Looking at the mdout file you attached, I see that the 1-4 VDW and 1-4 electrostatic (the latter shown as 1-4 EEL) energy terms are given as "NaN", as are the RMS gradient and the total energy. This likely means one of two things. Either two atoms in a 1-4 relationship are on top of each other -- in which case the denominators in the expressions for electrostatic and van der Waals terms go to zero -- or you have bogus parameters, typically a zero value where a non-zero value is expected. Since both electrostatic and van der Waals terms are affected, I'd suspect the former.
>
> In short, check your structure for overlapping atoms.
>
> Hope that helps,
> Ben
>
>
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--
Agostino Bruno, PhD
Dipartimento Farmceutico
Universita' degli Studi di Parma
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Received on Thu Mar 29 2012 - 01:30:03 PDT
