VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Nov 05 2007 - 07:11:28 CST

Hi Sam,

Molefacture has a maximum recursion depth that it uses in checking for
the atoms that should be rotated with a dihedral; I thought I'd chosen a
suitably large value, but apparently not (molefacture had originally
been geared toward relatively small structures). I'll send you a version
later today to test that sets this depth based on the molecule size, and
lets you flag which side of the molecule to move. The behavior in VMD
1.8.6 is to rotate whichever side of the molecule is smaller, which is
usually the "right thing" for small ligands, but I understand that as
people work on larger structures it's better to be able to choose.
Best,
Peter

Samuel Coulbourn Flores wrote:
> HI Guys,
>
> So I used molefacture to rotate the dihedral angles in my molecule.
> However the result of this is hard to understand. The dihedral angle
> targetted in fact changes, but instead of the entire molecule
> downstream rotating together, an (as far as i can tell) aritrary point
> is chosen at which to "break" the chain. Everything downstream of
> this break remains stationary. How can I make it so the entire
> molecule to one side of the dihedral rotates together? Even better
> would be to be able to choose which side of the molecule rotates and
> which side is the anchor.
>
> Many thanks,
>
>
> Sam
>
> On Nov 4, 2007, at 11:53 AM, John Stone wrote:
>
>> Hi,
>> It was posted just the other day, but for your convenience
>> I've attached a copy of it to this email. I'll update the
>> script library web page with this version since a lot of people
>> need it these days.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Sun, Nov 04, 2007 at 12:46:13PM -0700, Dong Xu wrote:
>>> Hi John, I remember you mentioned before about the
>>> bigdcd_wait_until_done script. Could you tell me where I can download
>>> it from? I have a 50GB trajectory file. bigdcd didn't work well, it
>>> only processed a few hundreds frame and quit.
>>>
>>> Thanks,
>>> Dong Xu
>>>
>>> On 11/3/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>>>>
>>>> Hi,
>>>> Luis' RMSDTT plugin can do the both of the alignments you're
>>>> asking about
>>>> without having to write scripts etc. Please see the documentation for
>>>> it here:
>>>> http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/
>>>>
>>>> Read the section "calculation type", and "reference molecule" in
>>>> particular.
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>>>
>>>> On Thu, Nov 01, 2007 at 03:52:12PM -0600, Zhaochuan Shen wrote:
>>>>> Hi all,
>>>>>
>>>>> I have two quesiotns:
>>>>>
>>>>> 1) For all the scripts posted on the website and plugins about
>>>>> RMSD, there
>>>>> are feature about alignment. Why people want to do alignment? How
>>>>> people do
>>>>> this? The scripts are not very clear. Just "measure fit" and then
>>>>> "move".
>>>>> 2) I have a long trajectory (100000 frames) and want to find out RMSD
>>>>> for some alpha carbons. The reference is average coordinate. Is
>>>>> there any
>>>>> standard process? What I did is exprot the trajectory and then use
>>>>> RMSDTT
>>>>> plugin directly. Do I need to do the alignment? Or anyone can give a
>>>>> standard process? Thanks!
>>>>>
>>>>> Wishes,
>>>>> Zhaochuan
>>>>
>>>> --
>>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>>> Beckman Institute for Advanced Science and Technology
>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>>
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>> <mybigdcd.tcl>