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
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 12:09:59 PDT
