AMBER Archive (2006)

Subject: RE: AMBER: Atom Type problem

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Dec 08 2006 - 12:09:05 CST

Thanks Ross

That was the problem. If you ever get time to make that more complex
example on adding nonstandard residues, I certainly will go over it.

 

Thanks, again

Steve

 

________________________________

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Ross Walker
Sent: Friday, December 08, 2006 11:21 AM
To: amber_at_scripps.edu
Subject: RE: AMBER: Atom Type problem

 

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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|\oss Walker

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________________________________

        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
On Behalf Of Steve Seibold
        Sent: Friday, December 08, 2006 08:01
        To: amber_at_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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