Sounds like you might better stick with the compsci part of your program
if you're going to be insulting professors and really a whole community
of researchers in compchem, who will be reviewing any papers you write.
Bill
On 12/2/20 4:01 PM, Gordon Richard Chalmers wrote:
> I know you people, Carlos, from SB NY. You are supposed to work first
> and then talk. Figure it out before saying it is possible or not.
>
> Gordon Chalmers
> ________________________________
> From: Gordon Richard Chalmers <gordoncs.uga.edu>
> Sent: Wednesday, December 2, 2020 6:08 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] question about dihedral angles
>
>
> By the way, are you sure the angular rotation is about the
> 2 middle atoms in the 4 bond. That would be good to know if
> writing your own code.
>
> Gordon Chalmers
> ________________________________
> From: Gordon Richard Chalmers <gordoncs.uga.edu>
> Sent: Wednesday, December 2, 2020 5:58 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] question about dihedral angles
>
>
> Why don't you try this then: given phi psi angle information of
> pdb and a linear peptide of its form, reconstruct the pdb file.
> The problem is not due to numerical instability of the phi/psi
> angle computation; phi/psi angles are important physically.
>
> Gordon Chalmers
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Wednesday, December 2, 2020 5:52 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] question about dihedral angles
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
>
> I think that even if you have a list of phi/psi pairs and their values,
> it's pretty well known that small angle variations can result in large
> Cartesian changes far from the bond being rotated. I'm not saying this
> isn't a good plan, but you may run into issues (as you say) with non-planar
> groups giving small changes in the intended dihedral and leading to
> significant changes farther down the chain.
>
> You should be able to put together a cpptraj script by listing the atom
> names/residues in dihedral commands to measure them from your pdb, then
> building a cpptraj script to rotate.
> Dan's documentation is quite good for academic code standards and I don't
> think you'll need him to make the inputs for you.
>
> tleap can do similar things with commands such as "impose", and in the end
> it should matter which part gets rotated if you have a single molecule,
> since all that will be affected is the overall rotational frame of
> reference. If that is important though, then Dan's suggestion is worth
> trying. There may be other codes that were intended to build structure
> models, Amber doesn't really have extensive tools for that purpose.
>
> On Wed, Dec 2, 2020 at 5:41 PM Gordon Richard Chalmers <gordoncs.uga.edu>
> wrote:
>
>> Hi Daniel,
>>
>> How about giving me a known PDB protein model and a sequence of
>> rotations to bring its linear form into it? That would be a benefit,
>> Either
>> in tleap or cpptraj.
>>
>> I think I know what the issue is with non-parallel planes from
>> the 2 pairs of 3 atoms in the 4 bond of the peptides.
>>
>> Gordon Chalmers
>> ________________________________
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Sent: Wednesday, December 2, 2020 11:50 AM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] question about dihedral angles
>>
>> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>>
>>
>> Hi,
>>
>> The command for calculating dihedral angles in cpptraj is 'dihedral'.
>> The command for rotating atoms around a dihedral is 'rotatedihedral'.
>> Both are documented in the manual. The convention in cpptraj is for
>> all atoms connected to the greater atom index to move; those connected
>> to the lower atom index are fixed. Cpptraj does the rotation in
>> Cartesian space - I think tleap may do it via internal coordinates but
>> I'm not sure about that.
>>
>> -Dan
>>
>> On Wed, Dec 2, 2020 at 9:04 AM Gordon Richard Chalmers <gordoncs.uga.edu>
>> wrote:
>>>
>>> Thank you for the help in this.
>>>
>>> In a protein the phi and psi angles require 2 adjacent
>>> residues. Calculating these angles and rotating is
>>> fairly easy. It is a matter of what is rotated to agree
>>> to a PDB model starting from a linear backbone model.
>>>
>>> I will be working the angle rotations further in tleap today,
>>> a little delayed at the moment.
>>>
>>> In principle, you should rotate the entire peptide chain
>>> after or before the ith residue as these are bonded in
>>>
>>> %% phi C(i-1)-N-CA-C
>>> %% psi N-CA-C-N(i+1)
>>>
>>> The actual rotation angle about the intermediary N-CA
>>> or CA-C axis should be the dihedral angle geometrically.
>>>
>>> Maybe my own Matlab algorithms aren't correct yet, but
>>> I have checked this many times. I will try to use tleap or
>>> cpptraj instead as a check.
>>>
>>> Gordon Chalmers
>>> Department of Computer Science
>>> Complex Carbohydrate Research Center
>>> University of Georgia
>>> ________________________________
>>> From: David A Case <david.case.rutgers.edu>
>>> Sent: Wednesday, December 2, 2020 8:51 AM
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Subject: Re: [AMBER] question about dihedral angles
>>>
>>> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>>>
>>>
>>> On Wed, Dec 02, 2020, Karl Kirschner wrote:
>>>> impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
>>> One point is this: the command above doesn't specific which atoms are to
>>> be *moved* in order to make the dihderal be 120 degrees. Should the
>>> program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
>>> to it)? Or do something else? This may not be important in some
>>> workflows, but can be key in others.
>>>
>>> The pyMol example has the same problem. Of course, its
>>> documentation may be better in explaining what choices are made.
>>>
>>> These sorts of manipulations are a natural for NAB (aka "molecular
>>> awk"), but it has its own learning curve and documentation deficiencies.
>>>
>>> ....dac
>>>
>>>
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