[gmx-users] Position restraint problem

[David]

On Wed, 2002-11-27 at 23:30, Arpita Aravind wrote:
> Hi David,
> Thank you for your reply. 
> On performing energy minimization the potential energy
> decreases from ~ 5e+09 kJ/mol to -1e+06 kJ/mol, hence
> one would assume that all bad Van der Waals contacts
> are removed. However, after energy minimization, on
> performing a short MD with position restraint on the
> heavy atoms and using 'gmxcheck' to analyze the
> trajectory file, a large number of carbon atoms are
> printed out. I have listed a few of them below:
> 
> atom# name  residue r_vdw  atom# name  residue r_vdw 
> distance
>    77   CG HISA   8 0.15      81  CE1 HISA   8 0.15  
> 0.2183
>    80  CD2 HISA   8 0.15      81  CE1 HISA   8 0.15  
> 0.2193
>   184   CG  TRP  21 0.15     190  CE2  TRP  21 0.15  
> 0.2335
>   185  CD1  TRP  21 0.15     187  CD2  TRP  21 0.15  
> 0.2255
>   185  CD1  TRP  21 0.15     190  CE2  TRP  21 0.15  
> 0.2284
>   269   CG HISA  28 0.15     273  CE1 HISA  28 0.15  
> 0.2168
>   272  CD2 HISA  28 0.15     273  CE1 HISA  28 0.15  
> 0.2189 
> 
> As can be observed from above, the distance between
> the atoms is less that the sum of both their Van der
> Waals radii. I cannot understand the cause for this.

Hm, have you check these with a tool like rasmol?
(set picking distance, and then click on the atoms).



-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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