On Thu, Mar 8, 2012 at 11:21 AM, Lorenzo Gontrani <l.gontrani.caspur.it> wrote:
> I suppose that VMD displays a bond (or not) on the basis of an
> internal cutoff (how long are your bonds?).
Normal length for what they should be (C-C single bonds)
> But maybe I am wrong. In the newest version (1.9) you can also
> explicitly link two atoms, or you can use the topotools plugin ("topo"
> command in the VMD shell) to generate a topology.
Not really. I would like that the viewer describes the actual system
as it is simulated. Also saving the pdb file and going to CHIMERA,
those bonds are not shown. Before investing time in simulations I
would like to be sure that those bonds exist, whether or not
represented by a line.
francesco
>
> Lorenzo
>
>
> 2012/3/8 Francesco Pietra <chiendarret.gmail.com>:
>> Right, thank you.
>>
>> rdparm XXX.prmtop
>>
>> rdparm menu: bonds :RESIDOFINTEREST
>>
>> actually shows all the bonds that I had set in.
>>
>> Does VMD require a special command to also show these bonds? By simply
>> selecting the specific residues (new residues), the bonds confirmed by
>> rdparm are not seen. I am interested to also see the bonds
>> graphically.
>>
>> thanks
>>
>> francesco
>>
>> On Thu, Mar 8, 2012 at 9:42 AM, Lorenzo Gontrani <l.gontrani.caspur.it> wrote:
>>> Why don't you check the topology with rdparm (and its "bonds" command)?
>>>
>>> Lorenzo Gontrani
>>>
>>> 2012/3/8 Francesco Pietra <chiendarret.gmail.com>:
>>>> Hello
>>>>
>>>> Bonds were set in xleap (ambertools 1.5), between newly created
>>>> residues, with command:
>>>>
>>>> bond unitname.residuenumber1.atomnameX unitname.residuenumber2.atomnameY
>>>>
>>>> "check unitname" after each "bond" command revealed some contac
>>>> between certain atoms. Bond/angle parameters and unit OK. The log file
>>>> (verbosity 2) does not reveal anomalies. All involved residues are in
>>>> the same unit.
>>>>
>>>> When the obtained top/crd file are loaded to VMD, the bonds, set as
>>>> above indicated, are not seen, i.e., the two indicated atoms are not
>>>> connected by a line.
>>>>
>>>> What should I further check to check whether the bonds were established or not?
>>>>
>>>> thanks
>>>>
>>>> francesco pietra
>>>>
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>>>
>>>
>>>
>>> --
>>> =======================================
>>> Lorenzo Gontrani
>>> Research associate of EDXD group
>>> University of Rome "La Sapienza"
>>>
>>> GSM +39 338 7615798
>>> Email l DOT gontrani AT caspur DOT it
>>> Webpage: http://webcaminiti/gontrani.html
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>>
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>
>
>
> --
> =======================================
> Lorenzo Gontrani
> Research associate of EDXD group
> University of Rome "La Sapienza"
>
> GSM +39 338 7615798
> Email l DOT gontrani AT caspur DOT it
> Webpage: http://webcaminiti/gontrani.html
> =======================================
>
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Received on Thu Mar 08 2012 - 03:30:03 PST
