hi Francesco- what's your question? I'm not sure what you're asking.
about the warnings? these are probably ok unless you want it neutral.
carlos
On Tue, Apr 21, 2009 at 5:29 PM, Francesco Pietra <chiendarret.gmail.com> wrote:
> I must apologize for not having looked at the leap.log before. The
> relevant portion of the log:
>
>> impose model3 { 225 226 227 228 229 230 } { { "N" "CA" "C" "N" -40.0 } { "C" "N" "CA" "C" -60.0 } }
>> saveamberparm model3 impose_pore.prmtop impose_pore.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 4.999220 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
>
> I took the "atomname" specification from the amber archive
> http://structbio.vanderbilt.edu/archives/amber-archive/2006/2387.php
>
> francesco
>
>
>
> On Tue, Apr 21, 2009 at 9:44 PM, Carlos Simmerling
> <carlos.simmerling.gmail.com> wrote:
>> I was thinking you could do that if it was only the helix, and I meant
>> to build a perfect helix from sequence. not sure if impose works when
>> reading a pdb. I meant to build the helix alone and use that for the
>> reference, but if the system is more complicated then you should
>> probably use restraints.
>>
>>
>> On Tue, Apr 21, 2009 at 2:40 PM, Francesco Pietra <chiendarret.gmail.com> wrote:
>>> On Mon, Apr 20, 2009 at 8:46 PM, Carlos Simmerling
>>> <carlos.simmerling.gmail.com> wrote:
>>>> I think it might be easier with dihedral angle restraints. it depends
>>>> on the rest of the system- if it's just the one helix, you could use
>>>> the impose command in leap to make a continuous helix as a reference
>>>> for SMD.
>>>
>>> I begun from the last suggestion, recreating the protein (made of
>>> capped helices which had been before isolated from the whole protein),
>>> with commands "model1 = loadpdb" "model2 = load pdb" (where the two
>>> models had been aligned before) and "model3 = combine" the protein
>>> was inserted into a lipidic membrane.
>>>
>>> Then command
>>>
>>> impose model3 { 225 226 227 228 229 230 } { { "N" "CA" "C" "N"
>>> -40.0 } { "C" "N" "CA" "C" -60.0 } }
>>>
>>> Then, with command "solvatebox" it was hydrated. The prmtop and inpcrd
>>> opened in a viewer, WAT and lipid removed, the bent helix looks like
>>> (grossly) unaffected. The bending angle is still ca 40 degrees.
>>>
>>> Should straightening of the helix have been expected at this stage or
>>> the impose command will be felt on running MD simulations? Or, have i
>>> misunderstood everything?
>>>
>>> thanks for having a look at this message
>>>
>>> francesco
>>>
>>>
>>>>
>>>>
>>>>
>>>> On Mon, Apr 20, 2009 at 1:31 PM, Francesco Pietra <chiendarret.gmail.com> wrote:
>>>>> Carlos: late in thanking you. I had to fix hardware and software problems.
>>>>>
>>>>> Complex:
>>>>>
>>>>> phi Gly227C Gly228N Gly228CA Gly228C ca 78 degrees (positive)
>>>>>
>>>>> psi Gly228N Gly228CA Gly228C Gln229N -19 degrees
>>>>>
>>>>> In a cartoon view, two cylinders make an angle of ca 40 degrees,
>>>>> interconnected by 227 228. I would like to approximately straighten
>>>>> that, to get a continuous cylinder. In a helix view, phi should be
>>>>> turned anticlockwise to reach at least the value -80 degrees (the
>>>>> value of corresponding nearby dihedral is just -80 degrees, while
>>>>> farther away it takes normal values, -57 degrees). psi, at least, has
>>>>> the correct sign.
>>>>>
>>>>> The bent helix is capped on both sides, but there are other similar,
>>>>> capped helices around, so that I guess the work should be carried out
>>>>> on the whole model. If I could restrain the capping groups alone of
>>>>> the bent helix (while finding a way that helicity, where correct, is
>>>>> conserved) I could imagine that straightening could occur. Otherwise,
>>>>> if all amino acids, except 227 228 of the bent helix, are restrained,
>>>>> how could the helix get straightened? Is that a task for SMD at all?
>>>>>
>>>>> thanks
>>>>> francesco
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Mar 30, 2009 at 1:56 PM, Carlos Simmerling
>>>>> <carlos.simmerling.gmail.com> wrote:
>>>>>> francesco, I think dihedral restraints may be the only way to go without a
>>>>>> helical ref structure. you'd definitely want to also restrain all other
>>>>>> residues in this helix to maintain it, or else you might just move the bend.
>>>>>> when changing the restraints over time, give thought to which direction to
>>>>>> rotate, which depends on the initial conformation of the Gly residues, if
>>>>>> they are currently adopting positive phi values then it's more complex than
>>>>>> just going from pp2 to alpha, for example, where you can just reduce psi.
>>>>>>
>>>>>> On Mon, Mar 30, 2009 at 6:16 AM, Francesco Pietra <chiendarret.gmail.com>wrote:
>>>>>>
>>>>>>> Hi:
>>>>>>> I would like to modify the conformation of a protein at one helix,
>>>>>>> which is bent at a region of three amino acids, Ile, Gly, Gly. Viewed
>>>>>>> in cartoon representation, it is constituted of two straight portions
>>>>>>> interconnected through a largely non helical set of the three amino
>>>>>>> acids.
>>>>>>>
>>>>>>> I would appreciate suggestions how to get the three aa taking part to
>>>>>>> the well ordered helical conformation, so that what is now (in
>>>>>>> cartoon) two straight portions interconnected by something like a loop
>>>>>>> becomes a wholly straitened motif. Rotation about dihedrals? Make the
>>>>>>> process with the isolated helix or in the whole context of the
>>>>>>> protein?
>>>>>>>
>>>>>>> I guess that steered MD (on which I have no experience) is the
>>>>>>> approach in Amber, though I wonder how to provide the target.
>>>>>>> Possibly, any biased MD should be carried out in explicit medium. In
>>>>>>> my hands, continuum models were unsuccessful with this protein.
>>>>>>>
>>>>>>> If these are not such naive questions to merit attention, thanks
>>>>>>>
>>>>>>> francesco pietra
>>>>>>>
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Received on Wed May 20 2009 - 12:10:01 PDT
