So, you didnt tell me whether you were trying to load a PDB file or a
combination of toppology/coordinates files ?
VMD 1.8.5 uses already a more complicated algorithm to assign bonds
than the one in older VMD version ... so in principle your PDB should
load fine in 1.8.5 ...
But if you didnt do it yet, i would still try to check by loading a
topology/coordinates combination into VMD and only if that produces the
same result, I would definetely check the structure ...
cheers
vlad
deepti nayar wrote:
> thank you sir
>
> I will use the recent version of vmd now. i was using vmd 1.8.5 right
> now. do you think even this version would create problems?I am asking
> this because if this is not the case, then i have to look into the
> xleap built structure as according to me, there is nothing wrong with
> th dipeptide
>
>
> thanks
>
> On 4/10/07, Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
>
>> Hi Deepti,
>>
>> which version of VMD are you using?? Did you try to load the .top and
>> .crd files or only the .pdb file ?
>>
>> Old versions of VMD would add bonds based on a trivial distance
>> criteria, so if you load a pdb file into an old VMD version, you will
>> get some "strange" bonds , especially since the structure created with
>> Leap is not a minimized structure ...
>>
>> My advice is to try to load into VMD the initial topology and coordinate
>> files created by Leap instead of the pdb file. If the visualization will
>> show you again strange bonds, then it is likely that something is wrong
>> with your structure ....
>>
>> If I were you, I would also use VMD 1.8.6 - the latest VMD version ...
>>
>> Good luck
>> vlad
>>
>>
>>
>> deepti nayar wrote:
>>
>> > hi
>> >
>> > I have made a dipeptide using xleap. my peptide is a non-standard
>> > residue and so i saved the library first and then made the structure.i
>> > have added suitable bonds and atoms as per my requirement. but when i
>> > visualize it using vmd, i could see some unnecessary bondings there. i
>> > was wondering if there is some mistake in the structure that i built
>> > using xleap. its a phenylalanine-dehydrophenylalanine dipeptide.(i
>> > have added the double bond between alpha carbon and beta carbon in
>> > dehydrophenylalanine)
>> >
>> > i would be obliged if somebody tells me where is the problem
>> >
>> > thanks
>> >
>> -----------------------------------------------------------------------
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>>
>> --
>> ----------------------------------------------------------------------------
>>
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>>
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
> -----------------------------------------------------------------------
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--
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------
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The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
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Received on Wed Apr 11 2007 - 06:07:36 PDT
