RE: AMBER: Atom Type problem

From: Ross Walker <>
Date: Fri, 8 Dec 2006 08:21:19 -0800

Dear Steve,
> 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
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| <> | PGP Key
available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.



From: [] On Behalf Of
Steve Seibold
Sent: Friday, December 08, 2006 08:01
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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Dec 08 2006 - 16:53:37 PST
Custom Search