roar-cp problems

From: M. L. Dodson <bdodson_at_scms.utmb.EDU>
Date: Wed 18 Dec 2002 15:00:37 -0600 (CST)

Hello all,

I have a problem with roar-cp that I cannot find addressed in its
manual. I have visited the Merz web site, but cannot find an email
address set up to answer questions. So I'll try here.


The behavior I'll describe seems to be the same whether I use the
99 or 94 FF parameters.

Amber7 (roar-cp was compiled and that worked).

The system is similar the HCA2 coupled QM/MM example, but with a
combined DNA/enzyme system (hydrogens included). Input coordinates
were from a 1000ps free MD run with sander (completely standard

I used carnal to cut out a water cap of 15A radius from the last frame
of the trajectory. I identified the cations within the cap and left
them in. I used leap to regenerate a new set of cations (two tries:
each of IB and K+). None of the newly placed cations overlapped any of
the cap waters. Saved the top and crd file after setting the cap
attribute for the system (proper center coords and radius were used).

When I ran roar-cp, it gave me an error message similar to: "unable to
identify element" for the K+ cations. Behavior was the same whether I
used K+ or IB for the added cations. OK, maybe roar-cp doesn't like
K+. So I repeated things leaving all the cations out. Leap complained
about the -19 net charge on the system, but I forged ahead. Now
roar-cp gives the following death declaration (actually all runs ended
this way, but I thought the base problem was the K+):

------ begin cut and paste

 begin time read from input coords = 0.000 ps

             BOX LENGTH = 0.00000 0.00000 0.00000
                         FATAL ERROR
          Link atoms MUST be optimized before MD run
------ end cut and paste

Ok, but how do I optimize the link atoms? And why does the HCA2
example work without this message? I haven't made any changes I
can think of that might cause different link atom behavior between
the example and my runs. The input coords I'm using are from leap.

I've read the manual until near blindness and still get no joy. Can
anyone help (with either the K+ or the link atoms problem)?

Thanks in advance,
Bud Dodson

M. L. Dodson                      
409-772-2178                                FAX: 409-772-1790
Received on Wed Dec 18 2002 - 13:00:37 PST
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