Dear Daniel,
I had used > radial ra.rdf 0.1 15 :1.C:DBR volume , cause I did find it in that way in the following tutorial.
http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml
1) Create an input file ptraj.in
trajin <trajectory filename>
radial CH3CN_N1 .1 15.0 :ACN.N
Or that this mean that it will calculate the RDF for the mask :ACN.N to any molecule around ??
I did calculate the RDF as you suggested " :DBR :1 ", unfortunately. I got something quite strange
#Distance_(Ang) :1_=>_:DBR
0.050 16.195501
0.150 623.214620
0.250 67.203886
0.350 0.000000
0.450 0.000000
0.550 0.000000
0.650 0.000000
0.750 0.000000
0.850 0.000000
0.950 0.000000
1.050 0.262508
1.150 14.017840
1.250 11.949163
1.350 0.100573
1.450 0.000000
1.550 0.000000
1.650 0.002517
1.750 1.470818
1.850 8.345936
1.950 1.211908
2.050 0.002650
I assume that because I am studying a solvent, I must be more careful with the mask.
therefore I did try :1.C :DBR.C, which gave me more "natural" results.
#Distance_(Ang) :1.C_=>_:DBR.C
0.050 0.000000
.................................
3.050 0.000461
3.150 0.001295
3.250 0.014602
3.350 0.052300
3.450 0.118061
3.550 0.245445
3.650 0.398117
3.750 0.524928
3.850 0.666235
3.950 0.799607
4.050 0.907142
4.150 0.977638
4.250 1.113866
4.350 1.193206
4.450 1.281679
4.550 1.289289
4.650 1.300614
4.750 1.282509
4.850 1.303025
4.950 1.283609
5.050 1.300981
5.150 1.310073
5.250 1.299347
5.350 1.327120
5.450 1.339304
5.550 1.329311
5.650 1.266836
5.750 1.211623
5.850 1.177190
5.950 1.091241
6.050 1.051369
6.150 1.012472
6.250 0.977152
6.350 0.946619
6.450 0.900090
..............................................
9.150 1.028306
Any advise that I should follow?
Also, how do I save the average density of the calculations ?
cpptraj -i x
run
write density1 ????
Thanks in advance
-------- Original Message --------
Subject: Re: [AMBER] Correctly defining keywords in cpptraj - radial
Local Time: October 13, 2016 12:41 PM
UTC Time: October 13, 2016 12:41 PM
From: daniel.r.roe.gmail.com
To: AMBER Mailing List <amber.ambermd.org>
On Wed, Oct 12, 2016 at 6:45 PM, Stregone <stregone.protonmail.com> wrote:
> confirm that my script is correct, cause I am getting some estrange results. Unfortunately, I did not find answer in the AMBER mail list regarding to my issue.
>
> # script
> parm prmtop
> trajin mdcrd
> radial r.rdf 0.1 15 :1 :DBR volume center1
> (this is for calculating the rdf from the residue 1[mask1] to any DBR [mask2] residue)
When calculating the RDF the order in which you specify masks matters.
In general, you want the first mask to be the one containing more
entities, so in this case you probably want the order to be ':DBR :1'
(see the manual for further details).
>
> radial ra.rdf 0.1 15 :1.C:DBR volume
> (if I understood correctly, this is for finding from the C atom in the residue 1, atom that belong to DBR residue)
Looks like you might be missing a space between ':1.C' and :DBR (as it
is it is not a valid mask). Also, as above, you probably want ':DBR
:1.C'.
>
> radial radi.rdf 0.1 15 :1:DBR volume center1
Again, you need a space between :1 and :DBR. In that case it is the
same as the first command.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 14 2016 - 05:30:04 PDT
