RE: AMBER: atome type error

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 8 Dec 2006 07:51:29 -0800

Dear Steve,
 
I'm not quite sure what you mean "I created a library and all force field
parameters defining it". Nothing in your original description mentions
parameters. You say you built a library file which will define the atom
types, charges and topologies but don't mention anything about creating a
new 'frcmod' file and loading this into leap with 'loadamberparams'. This
will be needed in order to define all the missing parameters. The fact that
Leap stops at the can't find atom type error means that the mass and vdw
parameters have not been defined for this type. You need to at least define
these two parameters and probably bond, angle and dihedral parameters as
well if this atom is bonded to others. An example frcmod entry would be:
 
MASS
CU 65.36

BOND
NB-CU 70.000 2.05000
 
ANGLE
CU-NB-CV 50.000 126.700
 
DIHE
NA-NB-CU-NA 1 0.000 180.000 3.000

NONBON
CU 2.20 0.200
 
I realize there is no tutorial that strictly deals with this on the amber
tutorial pages. I was going to create a very indepth tutorial for setting up
LADH which as part of it would cover all of the issues with setting up new
residues as well as charge derivation etc. Unfortunately I haven't had time
to complete this yet and so there is still just a placeholder on the main
tutorial page. However, an older tutorial, that the new one is slated to
replace, is still available at:
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/
 
I hope this helps.
 
All the best
Ross

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  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Steve Seibold
Sent: Friday, December 08, 2006 07:09
To: amber.scripps.edu
Subject: AMBER: atome type error



Hello Amber

I have made an alternative residue which contains an atom type NX (my
creation) in a Histidine. I have created a library (i.e. OFF file) and a
force field file. When I "Check" unit, xleap shows no errors because I
loaded the library and force field. It says Unit is ok. Now, when I try to
create topology file I get the message "could not find type: NX". I don't
understand. I created a library and all force field parameters defining it.
I must be doing something obviously wrong. Can someone help me?

 

Thanks much, Steve




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Received on Fri Dec 08 2006 - 16:23:31 PST
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