VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Apr 03 2011 - 08:49:53 CDT

I forgot the mailing ist. sorry

---------- 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
>