Hi Brian,
thanks, no simulation is done yet. This is just a starting structure.
Senthil
By "not holding" do you mean it decreased during a constant pressure simulation? I think that's quite common behavior since the water boxes built by leap are generally quite low density (like 0.7 or something). An initial and rapid increase in density (i.e. decrease in volume) is pretty much par for the course with AMBER.
Brian
On Tue, Nov 8, 2011 at 1:18 PM, Senthil Natesan <sen.natesan.yahoo.com> wrote:
>Hi Jan-Philip,
>
>Thanks for the response. I visually inspected the system and side chain of one residue is almost
>out of the box.
>
>
>Senthil
>
>
>
>Huhu,
>
>just to be sure that this is not an "issue of wrong perspective": did
>you quantify the minimum distance between the complex and the box? How
>big is it, if not 8 Angstrom?
>
>Jan-Philip
>
>On 11/08/2011 06:24 PM, Senthil Natesan wrote:
>> Dear Amber Users,
>>
>> Greetings.
>>
>> I am trying to solvateOCT a protein-ligand complex, but the minimum distance between
>> the complex and the solvent box edge seems to be not holding at the expected level (8 A)
>> The protein-ligand complex is almost touching the box edge (pls see the attached image)
>> though I get the proper solvation with solvateBox.
>>
>>
>> The command used is
>>
>>
>> solvateOct complex TIP3PBOX 8.0
>>
>> I am not sure what is wrong ? your suggestions/comments will be appreciated.
>>
>> thanks,
>> Senthil Natesan
>>
>>
>>
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--
================================ Current Address =======================
Brian Radak : BioMaPS Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
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Department of Chemistry : Piscataway, NJ 08854-8066
radak004.umn.edu : radakb.biomaps.rutgers.edu
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Received on Tue Nov 08 2011 - 11:30:03 PST
