Re: [AMBER] problem w/ radial results

From: Thomas Cheatham III <>
Date: Wed, 22 Aug 2012 15:56:37 -0600 (Mountain Daylight Time)

> I have an explicit solvent simulation with 0.2 M salt. I am calculating the
> gofr of Cl- ions around the protein with the following command in ptraj:
> radial distCl 0.05 10 :Cl- :1-93 closest
> I am having results that do not make sense, the ions start to line up at
> around 0.175 A which is considerably lower than a H--Cl bond length. I
> checked the energy values to see if the atoms somehow clash, I found
> nothing indicative of that kind. I checked the trajectory in VMD, nothing
> looks like .175 A close.
> How can I fix that issue?

>From the information provided I cannot provide great insight. I just ran
a similar command with ions around DNA and obtained a very smooth plot
with distances starting around 2-2.5 A (for K+ / Cl-).

The plot you showed is rather bumpy and clearly not converged, that aside,
it does appear that short distances are showing up... You can add in the
keyword "prnlev 4" prior to the radial command and this will dump
information on what is triggering the small distance, but I recommend
*only* doing this for a small number of frames or you'll be overwhelmed
with output.

trajin traj 1 10 1
prnlev 4

When running ptraj, put the output/stderr to a file:

ptraj prmtop < >& radial.out

You'll see information like:

Atoms (1141, 1140), bin 74, distance 3.737
Atoms (1142, 1140), bin 234, distance 11.717
Atoms (1147, 1140), bin 87, distance 4.391
Atoms (1148, 1140), bin 291, distance 14.592

Now, one idea is that somehow the coordinates are getting messed-up prior;
are you perhaps imaging *after* doing an RMS fit? If so, this is an
error / incorrect usage. Alternatively, is there a mismatch between the
prmtop and coordinates? You could try adding the "noimage" keyword,
however I do not think this is the source of trouble. Also, make sure you
have a recent/bugfixed version of ptraj. I just ran with AMBER 12
AmberTools and it worked fine... I'll try earlier versions too to see
if I can reproduce the wierd behavior...

If you are completely stymied, send me a small portion of the trajectory
and prmtop off-list and I'll track it down.


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Received on Wed Aug 22 2012 - 15:00:02 PDT
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