[gmx-users] Cationic Dummy atom method

andrea andrea.spitaleri at iit.it
Thu Feb 20 10:36:18 CET 2014


I tried once to use the same method for my protein bearing Zinc ions. 
Everything works fine ... if you use posre setup :)
I got the same error as you said and I tried to fix this in different 
ways. However all the attempts failed so I went back to the classical 
restraints between Zn and residues coordinating.

just my little comment to this



On 20/02/2014 04:23, Justin Lemkul wrote:
> On 2/19/14, 3:24 PM, Williams Ernesto Miranda Delgado wrote:
>> Hello Gromacs users
>> I am trying to simulate a complexed zinc ion with the cationic dummy 
>> atom
>> method (Pang,1999) in Amber FF.
>> In this Method the Zinc-Ion is mimicked by a central uncharged Zinc 
>> (full
>> mass) atom and 4 tetrahedric dummys with 0.5 charge each and very small
>> mass (0.1).
>> I used the force field parameters reported in Pang, 2000 (only bond and
>> angle parameters reported), but when I performed steepest descendent 
>> (sd)
>> energy minimization of a protein:ligand complex with this zinc dummy
>> cation in the active site, the tetrahedral geometry got distorted.
>> On the other hand, when I try to minimize the energy of the system using
>> the conjugate gradient method (after the sd minimization) I get this
>> output:
>> Fatal error:
>> 30491 particles communicated to PME node 2 are more than 2/3 times the
>> cut-off out of the domain decomposition cell of their charge group in
>> dimension x.
>> This usually means that your system is not well equilibrated.
>> Could you please give me some advices?
> Both outcomes indicate an unstable topology, but without seeing it, 
> it's impossible to suggest what might be wrong.
> -Justin

Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
ORCID: http://orcid.org/0000-0003-3012-3557

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