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"
>
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> Email l DOT gontrani AT caspur DOT it
> Webpage: http://webcaminiti/gontrani.html
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Received on Thu Mar 08 2012 - 02:00:02 PST
