It wasn't spot on as far as I can tell.
Give an example of reconstructing a folded protein
state, i.e. a pdf bile, from the phi and psi angles. Then
I won't be sure you are a bunch of idiots.
Stupid does.
Gordon Chalmers
________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Wednesday, December 2, 2020 10:25 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Ok, beating this into the ground, maybe Carlos has better things to do
than try stuff out for a grad student?
https://news.stonybrook.edu/awards-and-honors/carlos-simmerling-receives-award-for-covid-19-research/
Team award:
Titled the Gordon Bell Special Prize for High Performance
Computing-Based Covid-19 Research, the award recognizes “outstanding
research achievement towards the understanding of the COVID-19
pandemic though the use of high-performance computing.”
BR
On 12/2/20 7:20 PM, Bill Ross wrote:
> Stupidly insulting btw, since Carlos's answer was spot on.
>
> BR
>
> On 12/2/20 7:15 PM, Bill Ross wrote:
>> 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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Phobrain.com
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Received on Wed Dec 02 2020 - 20:00:01 PST
