RE: AMBER: Atom Type problem

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 8 Dec 2006 08:21:19 -0800

Dear Steve,
 
>NONBON
> FE 1.20000 0.05000 0.00000
> LO 1.60000 0.20000 0.00000
> LC 1.85 0.12 0.0
 
You need to also provide nonbonded parameters for ALL new atom types. You
have no NX parameters here hence the error message. You can probably just
copy them from a similar Nitrogen atom type in the FF03 force field file
(parm99.dat).
 
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 08:01
To: amber.scripps.edu
Subject: AMBER: Atom Type problem



Hi Amber

I am sending the files that I am using. I am just trying to create prmtop
and an inpcrd file of this HIX residue (HIX.pdb). If you load the HIX.lib
,HIX.pdb, Modfrcmod2.all and leaprc.ff03 everything seems to be ok. All
atoms are accounted for and all types (and angles etc) are there also. But
if you try and “saveamberparm HIX HIX.prmtop HIX.inpcrd” you will get the
message “could not fine type: NX Parameter file was not saved”.

Could someone assist me or at least let me know what I am doing wrong?

 

 

Cheers, Steve




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Received on Fri Dec 08 2006 - 16:53:37 PST
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