AMBER Archive (2001)

Subject: water density and rdf calculations

From: thenmalar rathinavelan (thenmalrr_at_yahoo.co.in)
Date: Wed Apr 11 2001 - 05:02:59 CDT

Dear Amber users,
    I like to calculate water density around my dna
molecule. For that I used grid command in ptraj. But,
I like to know how to choose nx, x_spacing, ny,
y_spacing, nz, and z_spacing values.
  For example I used,
 grid water 3 0.5 3 0.5 3 0.5 :1-5431

1-5431 atom represent all the residues in the system.
Is it correct? or I have to use only the water
residues there. What is the effect of 3, 0.5, 3, 0.5,3
,0.5?
What are all the packages I can use to visualize the
water density.
                                   
  My next doubt is about the calculation of radial
distribution function of Na+ -P.For that I used the
following code,
  radial rdf_ 0.5 10 :88-5431 @P,Na+
                        |_______|______for water
                                |
                                |_______for P, Na+
I got only two outputs for this. That is the
filename_carnal.xmgr file is not generated.
In other two outputs, namely file_name_standard.xmgr
and filename_volume.xmgr I got three columns. I like
to know what are these columns stands for and what is
the difference between these three outputs.
 
  Anyone please tell me, wheather I am using correct
the codes or not.

Thank you very much in advance

Thenmalar

____________________________________________________________
Do You Yahoo!?
For regular News updates go to http://in.news.yahoo.com