AMBER Archive (2009)

Subject: Re: [AMBER] Am I doing the right thing

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Tue Jul 28 2009 - 20:35:09 CDT

1) Am I doing the right type of solvation. PDB file generated from .inpcrd
file do show the particular type of solvents.
2) While running the simulation with sander the molecule solvated with CHCL3
is taking lesser that half the time taken by molecules solvated in other
solvents. Why is it so.
3) I am unable to solvate my protein with 8M urea-water mixture. This
solvation is not similar to the others. Can anyone tell me how to solvate
with this solvent.

Hello nicholus,
1. I cant say it a correct solvation, Unless you are confident, what
you are attempting.
Better use solvateoct as they better define the confirmational geometry.
2. The time depends on the number of atoms included in the
calculation. CHCL3 has just 5 atoms involved for each residue. Rest
have a higher number.
3. see you can better use a mixed system. Add urea explicitly and then
go for implicit solvent minimization with igb=2, which will be better.

All the best,
Ashish

On Tue, Jul 28, 2009 at 10:50 PM, nicholus
bhattacharjee<nicholusbhattacharjee_at_gmail.com> wrote:
> Dear community,
>                          I am trying to simulate my protein in different
> type of solvents. The solvent models provided in Amber 9 other that water
> are MEOH, CHCL3, NMA etc. So I am solvating my molecule by the following
> procedure in leap
>
>> loadAmberParams frcmod.meoh/chcl3/nma
>> mol=loadpdb mypdb
>> solvateBox mol MEOHBOX/CHCL3BOX/NMABOX 10
>> charge mol
>> addIons mol (added charge as per)
>>saveamberparm mol pdb.prmtop pdb.inpcrd
>>quit
>
> These procedure is creating the parameter and the coordinate files. My
> questions are that
> 1) Am I doing the right type of solvation. PDB file generated from .inpcrd
> file do show the particular type of solvents.
> 2) While running the simulation with sander the molecule solvated with CHCL3
> is taking lesser that half the time taken by molecules solvated in other
> solvents. Why is it so.
> 3) I am unable to solvate my protein with 8M urea-water mixture. This
> solvation is not similar to the others. Can anyone tell me how to solvate
> with this solvent.
>
> Thanx in advance for answering the questions
>
> Sincerely yours
> Nicholus
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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