VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Apr 03 2011 - 09:14:44 CDT

I forgot not only the mailing list but also to say that straight
recovery of the whole ensemble, after rotation of a histidine
imidazole moiety, is to attribute to the position of the residue at
the external surface of the protein. Rotation of the imidazole moiety
had no opportunity to introduce major vdw repulsions.
francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sun, Apr 3, 2011 at 12:45 PM
Subject: Re: vmd-l: (my) problems using molefacture dihedral
To: Peter Freddolino <petefred_at_ks.uiuc.edu>

Hi Peter:
Thanks for this prompt help, weekend notwithstanding. Yes, my mistake
was to select four atoms, as for a dihedral, without reading
accurately the molefacture description. This morning the vmd web site
can't be reached from here but I am sure that the description leaves
no doubts about selecting two atoms only.

At any event, it works fine now. I had to select several residues
around HSD in order that just the imidazole moiety rotates. Saved pdb
and replaced those residues in the original pdb for the ensemble in a
solvated and neutralized box. Previous topology works fine together
with the new pdb and a minimization at 310 K had no problems.

thanks again
francesco

On Sun, Apr 3, 2011 at 2:05 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Francesco,
> Did you see the dihedral actually rotate in the vmd window?
> Your procedure sounds incorrect in that, to get molefacture to recognize
> a dihedral you need to have exactly two atoms selected, not four. When
> you do this for two bonded atoms, you should see yellow spheres show up
> highlighting other atoms involved in the dihedral, and then see the
> atoms move as you move the dihedral slider. Does this happen?
>
> Best,
> Peter
>
> On 04/02/2011 04:36 PM, Francesco Pietra wrote:
>> Hi:
>> I am unable to use molefacture correctly to change the value of a
>> dihedral for the side chain of histidine, i.e. rotating the branch
>> with the imidazole ring by some 90 degrees. I would be grateful for
>> correcting my procedure with vmd 1.9beta1 starting from either a pdb
>> or psf/pdb.
>>
>> (1) Load the molecule.
>> (2) Molefacture.
>> (3) select the residue HIS
>> (4) Pick the four atoms for the dihedral.
>> (5) Change the value of dihedral on the ruler.
>> (6) File > Apply change to parent.
>>
>> whereby I find  a molef_tmpfile_merge.xbgf where the dihedral is unchanged.
>>
>> Alternatively to (6)
>>
>> (7) Save .. pdb
>>
>> again no change to the dihedral.
>>
>> Sorry for posing such an uninteresting question.
>>
>> thanks for advice
>> francesco pietra
>