AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 16 2008 - 07:57:42 CST

I tried this tutorial and it works fine for me with AmberTools 1.2
please let us know exactly what tleap you are using, and perhaps send the
entire leap.log.
have all of the test cases passed? did you make any changes to the
ras-raf.pdb file? do you still have the TER line between residues 166 and
167?

On Sun, Dec 14, 2008 at 6:25 AM, Maryam Hamzehee <maryam_h_7860_at_yahoo.com>wrote:

> Hi
> As I mentioned before, I am running toturial A3 (MM-PBSA) in Amber website
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm, 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,
>
>
>
> Maryam
>
>
> --- On *Sat, 12/13/08, Carlos Simmerling <carlos.simmerling_at_gmail.com>*wrote:
>
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> Subject: Re: AMBER: problem with toturial A3 (MM-PBSA)
> To: amber_at_scripps.edu
> 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 <maryam_h_7860_at_yahoo.com
> > 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.
>>
>> Thanks
>> Maryam
>>
>>
>
>

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