[AMBER] about results

From: Carlos Romero <carlos.rom.74he.gmail.com>
Date: Fri, 12 Oct 2012 20:28:18 -0500

Hi all.

I am simulating a protein with ions (3be udesf from PDB.org + MG2 + 2Cl-)

I used the next procedure:

with parmcheck 3bef.pdb I have adapted my molecule, because tleap doesn't
accept it.

with SANDER I have minimized and then heat 3bef

I charge 3bef in tleap and with addions2 I added 74 MG2 ions and 148 Cl-
I solvated with TIP3PBOX 10.0 And save amberparm *.prmtop and *.inpcrd

with SANDER I did my simualtions. (I took mdin for minimizations and
dinamycs from tutorial 1 from ambermd.org)

every thing is okey until when I revised 3bef.pdb comparing with
3bef_wat_mgcl2_dm.pdb I observed that almost 80% of the residues are in

My question is: Is it ok? or Do I have did something wrong?

please if anyone could help me I will appreciate a lot.

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Received on Fri Oct 12 2012 - 18:30:03 PDT
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