AMBER Archive (2006)

Subject: Re: AMBER: impose command in leap problem

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Mon Aug 14 2006 - 15:44:02 CDT

Hi Scott
Thanks for some hints with that "impose" command for leap.

Switching from: impose aa {167 168} {{ CH3 C N CA 180.0 }}
into: impose aa {167 168} {{ "CH3" "C" "N" "CA" 180.0 }}
helped. I am not geting now any error messages from leap.

Unfortunately there is something more related to this command
that I don't understand.

I have a system consisting of protein and ligand.
I want to change the first peptide bond (between ACE-HIS) in ligand
from 0 degree (as built originally by leap) into 180.
When I try to do this for protein-ligand (using absolute - amber residue
numbering, 167-168) the angle is not changed. When trying to do the same
but only for the ligand, e.g. running leap setup for ligand only and using
also 167-168 for residue numbers(?), the angle is properly changed to 180.
Do you have any idea why it is so?

In attachment is setup for running my protein-ligand complex and ligand itself.

Is there any other, way for internal coordinates manipulation in amber now?

Thanks
Piotr

On Fri, 11 Aug 2006, Scott Brozell wrote:

> Date: Fri, 11 Aug 2006 18:57:21 -0700
> From: Scott Brozell <sbrozell_at_scripps.edu>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: impose command in leap problem
>
> Hi,
>
> On Fri, 11 Aug 2006, Piotr Cieplak wrote:
>
>>
>> Can anybody help with "impose" command in Leap?
>> When trying to impose dihedral angle spanning two residues (let's say:
>> 167-168) I tried to use the following:
>>
>> impose aa {167 168} { CH3 C N CA 180.0 }
>>
>> but I am getting the following error message:
>>
>> impose: Invalid internal in list
> ...
>> impose: Invalid internal in list
>>
>>
>> If I use something which looks slightly more like it is stated in
>> documentation:
>>
>> impose aa {167 168} {{ CH3 C N CA 180.0 }}
>>
>> leap complains:
>>
>> impose: Illegal angle internal definition
>> impose: Illegal angle internal definition
>
> According to the source these errors are caused by either one of these
> (CH3 C N CA) not being a string or by 180.0 not being a double.
> Both of these errors seem not to exist. Indeed,
> when I try the exact command above on a random unit there are no complaints:
> 1plc=loadpdb 1PLC_mod_final.pdb
> impose 1plc {167 168} {{ CH3 C N CA 180.0 }}
>
> You could try
> impose aa {167 168} {{ "CH3" "C" "N" "CA" 180.0 }}
>
> but something else is probably amiss.
> You can send me your input files.
>
> Scott
>
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