I suppose that VMD displays a bond (or not) on the basis of an
internal cutoff (how long are your 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.
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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> =======================================
>> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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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 - 02:30:03 PST
