[gmx-users] simulation of protein in presence of ATP

[Lucio Montero]

Independently of your ATP position, your system may explode or show 
LINCS warnings if you use pressure and temperature coupling. I had these 
problem, and corrected it removing the pressure coupling. Pressure 
coupling will let your system expand in response to the heat, and if the 
positions are restrained, it`s going to develop a big force that makes 
your system explode, as happens in real life.

nikhil damle escribió:
> Hi
>
> When i subjected the complex to EM, it gave following warning:
> "1-4 interaction between 3063 and 3068 at distance 1.436 which is 
> larger than the 1-4 table size 1.000 nm. These are ignored for the 
> rest of the simulation. This usually means your system is exploding,"
>
> These atoms are oxygens of 2 phosphate grps ofATP. Later if i 
> continue, with SD it converges with less precision. so i applied CG. 
> It converged. But when I carry out position-restrained dynamics, it 
> gave # of LINCS warnings in both cases. Does this mean EM is not done 
> properly ? How should I address this ?
>
> Regards,
> Nikhil
>
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, 23 June, 2009 9:10:15 PM
> *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
>
> nikhil damle wrote:
> > OK till here done ! the pdb file generated for EM should have ATP 
> molecule @proper position as input .top file has the ATP.itp included. 
> It did not have. If I do -ci it would randomly replace the solvent. I 
> want ATP @ its proper location. how do i do this ?
>
> Like I implied several emails ago, you should order the [molecules] 
> entries according to the coordinate file, as normal.
>
> Mark
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-- 
Lucio Ricardo Montero Valenzuela
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210