[AMBER] average structure

From: aneesh cna <aneeshcna.gmail.com>
Date: Mon, 22 Nov 2010 11:31:11 -0500

Dear amber users,

           I am doing a simulation of DNA in water using Amber 9.0 version.
I am try to get a average structure of solvated DNA over the last 3 ns with
an aim to see the average position of water molecules within the first
salvation layer of DNA, using the the following script in Ptraj

trajin ../27md.crd
trajin ../28md.crd

center :289-300 mass origin
image origin center
center :289-312 mass origin ( 289 to 312 for DNA molecules)
image origin center

rms first mass out rms.dat :289-312

average average.pdb pdb


But in the average structure water forms big blob in the center of the DNA.
When I try to do few steps of minimization, run terminated with an error as
shown below....

* NB pairs 5449 26125589 exceeds capacity ( 26125624)
     SIZE OF NONBOND LIST = 26125624
 SANDER BOMB in subroutine nonbond_list
 Non bond list overflow!
 check MAXPR in locmem.f

Can anyone help me to figure out what went wrong with the calculation?

Thanks in advance

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Received on Mon Nov 22 2010 - 09:00:04 PST
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