Hi Dan,
I’m running AmberTools 13. I’ve prepared numerous parameter files in the last few days without problem.
In fact, I’ve run a 100ns MD simulation and what I’m trying to do is to generate new parameter files keeping a conserved water molecule in the topology of the receptor. The reason for this is to run MMPBSA making sure that the water molecule is not stripped.
Regards
George
On 1Dec, 2014, at 5:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> What version of AmberTools are you running, and what updates have been
> applied? Do all tests pass?
>
> -Dan
>
> On Monday, December 1, 2014, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I’m trying to generate parameter files for a protein.
>>
>> lteap generates top and crd files for the COMPLEX. The complex has two
>> ligands and one water molecule
>>
>> saveamberparm COMPLEX 3n7h_de4.top 3n7h_de4.crd
>> Checking Unit.
>> WARNING: The unperturbed charge of the unit: -9.002004 is not zero.
>>
>> -- ignoring the warning.
>>
>> Building topology.
>> Building atom parameters.
>> Building bond parameters.
>> Building angle parameters.
>> Building proper torsion parameters.
>> Building improper torsion parameters.
>> total 406 improper torsions applied
>> Building H-Bond parameters.
>> Incorporating Non-Bonded adjustments.
>> Not Marking per-residue atom chain types.
>> Marking per-residue atom chain types.
>> (Residues lacking connect0/connect1 -
>> these don't have chain types marked:
>>
>> res total affected
>>
>> CVAL 1
>> DE3 1
>> DE4 1
>> NASP 1
>> WAT 1
>> )
>> (no restraints)
>>
>>
>> The receptor has one ligand and one water molecule. But when I try to load
>> the protein and generate parameters I get. Any suggestions how to overcome
>> this problem would be most welcome
>>
>> /Programs/amber12/bin/tleap: line 17: 1888 Segmentation fault: 11
>> $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib
>> -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Mon Dec 01 2014 - 12:30:03 PST
