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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Received on Thu Mar 08 2012 - 04:00:03 PST
