On Thu, Mar 8, 2012 at 3:27 PM, francesco oteri
<francesco.oteri.gmail.com> wrote:
> 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?
There is everything in prmtop-inpcrd, the problem is to read in as
text without ad hoc studies.
I tried with psfgen: what present in psfgen is shown by VMD. Either it
is not the same with top--crd/VMD or I did something wrongly. At any
event, rdparm shows the bonds.
francesco
>
> 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 - 10:30:03 PST
