[AMBER] Fwd: vmd-l: Re: Viewing with VMD bonds set by the "bond" command

From: Francesco Pietra <chiendarret.gmail.com>
Date: Fri, 9 Mar 2012 08:39:17 +0100

It seems to me now that it is a general feature of VMD not displaying
bonds established within LEaP with command "bond". At least not so by
merely selecting the atoms/residues at issue, as I did with my system.

If you take the old Ross Walker's Tutorial A1 with plastocyanin (More
Advanced Version)
and load into VMD 1PLC.prmtop and 1PLC.inpcrd (available on that web
page), you can see that there is no line joining the copper atom with
the nitrogen of histidine (a bond that was set in with command
"bond"). In contrast, N-metal bonds established in p2n R.E.D. files
are displayed by VMD (as with my system).

Later on, in a new Tutorial A1 on anchoring fluorescein to DNA
<http://ambermd.org/tutorials/advanced/tutorial1/section1.htm>, Ross
Walker et al made recourse to code Sirius to attach covalently the
ligand. I have not read the Tutorial in full but, on loading to VMD
fam5_polyat top/crd, the bond is shown.

Thus, if the above is correct (I confess that I have not studies the
matter thoroughly), how to set the bonds that one would like to see
with VMD? Make recourse to something else than the LEaP's "bond"
command? Are all bonds detected by rdparm (i.e., written into prmtop)
treated the same way during MD? It should be "yes".


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Thu, Mar 8, 2012 at 7:27 PM
Subject: vmd-l: Re: [AMBER] Viewing with VMD bonds set by the "bond" command
To: AMBER Mailing List <amber.ambermd.org>, vmd-l.ks.uiuc.edu

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
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> --
> Cordiali saluti, Dr.Oteri Francesco
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Received on Fri Mar 09 2012 - 00:00:03 PST
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