AMBER Archive (2008)

Subject: Re: AMBER: How to create *.top & *.crd file with hexagonal lattice

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Nov 18 2008 - 08:05:12 CST

On Sun, Nov 16, 2008, Chin, Keith B wrote:
>
> Here're my procedures to create the ice *.top and *.crd file from my pdb file in xleap:
>
> 1. > ice = loadpdb ice.pdb
> 2. > setbox ice vdw 1.0
> 3. > saveamberparm ice fn.top fn.crd
> 4. Then, I manually changed the last line in *.crd file from alpha = 90
> degrees, beta = 90 degrees, and gamma = 90 degrees to with alpha = 90
> degrees, beta = 90 degrees, and gamma = 120 degrees
>
> However, upon this manual change in *.crd file, sander does not seem to like
> it and errors out when I try to run my MD sim. The only change is the gamma
> angle from 90 to 120.
>
> My MD output error is:
>
> FATAL: Could not read velocities from Ice_TIP4P_216_3.crd

This doesn't seem to have anything to do with the gamma angle. Rather, it
looks like you should check the value of ntx you are using. If you don't have
velocities in your input file, then ntx should be set to 1.

...dac

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