AMBER Archive (2009)

Subject: [AMBER] Am I doing the right thing

From: nicholus bhattacharjee (
Date: Tue Jul 28 2009 - 12:20:57 CDT

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

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
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