AMBER Archive (2005)

Subject: Re: AMBER: Solvate question?

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Mon Jun 06 2005 - 11:13:37 CDT


those have space too, just smaller. more complicated solvents
sometimes use larger space to avoid solvent molecule overlap,
I am not sure how that box was built but equilibrating it
should get rid of the problem.

Anthony Cruz wrote:

>But I try it with water (TIP3PBOX) and methanol (MEOHBOX) and I don have this
>problem. With both themolecule was solvated complidly, in contrast with the
>acetonitrile box ther is space between the solvent!!
>
>On Monday 06 June 2005 7:26 am, Carlos Simmerling wrote:
>
>
>>try starting with a larger box and then equilibrating the sovent while
>>restraining the protein (at constant P, check the archives since people
>>ask this often about water boxes).
>>
>>Anthony Cruz wrote:
>>
>>
>>>Hi user:
>>>I try to solvate my protein with the acetonitrile model in
>>>http://pharmacy.man.ac.uk/amber/. I download ch3cn_210.pdb, prep.ch3cn
>>>and frcmod.ch3cn. I load ch3cn_210.pdb (mecn=loadpdb ch3cn_210.pdb),
>>>prep.ch3cn (loadAmberPrep prep.ch3cn) and frcmod.ch3cn (loadAmberParams
>>>frcmod.ch3cn) in leap and the I try to solvate my protein solvateBox
>>>protein mecn 8.0. When I see the results the protein was not solvated
>>>completely, their is some empty spaces between the solvent. How I could
>>>solvate the protein???
>>>
>>>Anthony
>>>
>>>
>>-----------------------------------------------------------------------
>>
>>
>
>
>
>
> ------------------------------------------------------------------------
>

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor           Phone: (631) 632-1336
Center for Structural Biology Fax:   (631) 632-1555
Stony Brook University        Web:   http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115    E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

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