AMBER Archive (2008)

Subject: Re: AMBER: problem with toturial A3 (MM-PBSA)

From: Maryam Hamzehee (
Date: Sun Dec 14 2008 - 05:25:00 CST

As I mentioned before, I am running toturial A3 (MM-PBSA) in Amber website, in order to calculate the binding energy of the RAS-RAF protein complex but in the first step I have a problem in building the files related to RAS-RAF protein complex. I used the following commands,
> $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

com = loadpdb ras-raf.pdb
ras = loadpdb ras.pdb
raf = loadpdb raf.pdb
saveamberparm com ras-raf.prmtop ras-raf.inpcrd
saveamberparm ras ras.prmtop ras.inpcrd
saveamberparm raf raf.prmtop raf.inpcrd
The files ras-raf.prmtop ras-raf.inpcrd related to RAS-RAF protein complex can not be produced. The following error has been observed.
saveamberparm com ras-raf.prmtop ras-raf.inpcrd
Checking Unit.
WARNING: There is a bond of 39.885325 angstroms between:
-------  .R<HIP 166>.A<C 17> and .R<ASN 167>.A<N 1>
FATAL:  Atom .R<HIP 166>.A<OXT 19> does not have a type.
FATAL:  Atom .R<ASN 167>.A<H1 15> does not have a type.
FATAL:  Atom .R<ASN 167>.A<H2 16> does not have a type.
FATAL:  Atom .R<ASN 167>.A<H3 17> does not have a type.
Failed to generate parameters
Parameter file was not saved.

Thank you in advance for any help,

--- On Sat, 12/13/08, Carlos Simmerling <> wrote:

From: Carlos Simmerling <>
Subject: Re: AMBER: problem with toturial A3 (MM-PBSA)
Date: Saturday, December 13, 2008, 7:05 PM

please send exactly what you tried to do and the exact messages that the program gave you. also check the leap.log file for any warnings or errors and include that.
it's very hard to help when we can't see what happened.

On Sat, Dec 13, 2008 at 10:22 AM, Maryam Hamzehee <> wrote:

Dear Amber Users
I am trying to run toturial A3 (MM-PBSA) but I have problem in building the structures  related to complex of ras-raf .pdb (i.e. ras-raf.prmtop ras-raf.inpcrd) using saveamberparm com ras-raf.prmtop ras-raf.inpcrd command. The "saveamberparm" command does not generate mentioned structures. Any help in this regard would be higly appreciated.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)