Hi Francesco,
If I remember well in the prmtop there is a section where bonds are listed.
Could you directly inspect such a section to see if the atomic indexes are
there present?
Francesco
Il giorno 08 marzo 2012 12:48, FyD <fyd.q4md-forcefieldtools.org> ha
scritto:
> Francesco,
>
> >> if you load two prmtop/prmcrd files (or a mol2 file) into VMD a bond
> >> (if it is correctly defined) should be displayed independently of its
> >> length.
> >
> > OK. Suppose VMD has no faults (last edition). How to explain, however,
> > that "rdparm", through its "bonds" command, shows the bonds while
> > prmtop/inpcrd in VMD does not? Suppose the bonds are not correctly
> > defined, how to explain that "rdparm" shown them at a correct bond
> > length?
>
> I do not explain that; but for sure this has to be understood before
> running MD simulations ;-)
>
> Once again I would do a simple test using a basic model (and not a big
> protein) to understand what's going on...
>
> Or send to my personal email your prmtop/prmcrd files with the
> corresponding LEaP script, where the bond command(s) are reported...
>
> regards, Francois
>
>
>
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--
Cordiali saluti, Dr.Oteri Francesco
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Received on Thu Mar 08 2012 - 06:30:04 PST
