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

[Justin A. Lemkul]

nikhil damle wrote:
> 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 ?
> 

Some useful links:

http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

http://oldwiki.gromacs.org/index.php/blowing_up

-Justin

> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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