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

nikhil damle pdnikhil at yahoo.co.in
Wed Jun 24 11:23:44 CEST 2009


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 ?


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.

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