Hi Jason,
Please ignore my previous question.
I was able to get it to work.
Thanks!
On Thu, Jul 31, 2014 at 9:46 PM, Vivek Shankar Bharadwaj <
vbharadw.mymail.mines.edu> wrote:
> Hi Jason,
>
> So Should I strip the IL residues from the mdcrd also?
>
> I already removed the ILs to get my complex.prmtop using the strip_mask
> (-s)
>
> Vivek
>
>
> On Thu, Jul 31, 2014 at 9:33 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Thu, Jul 31, 2014 at 11:07 PM, Vivek Shankar Bharadwaj <
>> vbharadw.mymail.mines.edu> wrote:
>>
>> > Hi Jason,
>> >
>> > Some more Info.
>> >
>> > The number of atoms in the (complex) = number of atoms in (receptor +
>> > ligand) topology files.
>> > However, I am running a simulation of an enzyme in an ionic liquid water
>> > mixture. I did consider the IL to be part of the solvent and stripped it
>> > when getting the complex prmtop.
>> >
>> > Could this have anything to do with the NATOM mismatch?
>> >
>>
>> Probably. You probably have to change the "strip_mask" variable to strip
>> the IL residues out of your system if you didn't include them in your
>> topology file.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
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>>
>
>
>
> --
> Vivek S. Bharadwaj
> Graduate Student
> Department of Chemical and Biological Engg.
> Colorado School of Mines
> Golden Colorado
>
--
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Thu Jul 31 2014 - 21:00:03 PDT
