Re: [AMBER] Viewing with VMD bonds set by the "bond" command

From: FyD <>
Date: Fri, 09 Mar 2012 19:10:27 +0100


In your P6608-leap_fixed2.ff, replace:
        { "ZN" "Zn" "sp3" }
        { "Zn" "Zn" "sp3" }

Indeed, your atom type is Zn & not ZN...
This allows removing many error messages in the X-terminal (not in LEaP)

then, create prmtop/prmcrd files with or without your three bonds:

PROT = loadpdb prot_renumb_fixed.pdb
# Without bond
saveamberparm PROT PROT1.crd

bond PROT.253.CA PROT.365.C30
bond PROT.166.CA PROT.365.C15
bond PROT.164.CA PROT.365.C5
# With bond
saveamberparm PROT PROT2.crd

diff PROT1.crd PROT2.crd
-> same files: OK
-> different files: OK

finally load each prmtop/prmcrd files as a single molecule in VMD;
-> display only the MOL, ACT and BKB residues...

- when the 3 bonds are _present_ in the prmtop file, they are indeed
displayed as they should be.
- when the 3 bonds are _absent_ in the prmtop file, they are NOT
displayed as they should be.

So all is fine in the best of the world ;-)

regards, Francois

> 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
> <>, 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".
> francesco
> ---------- Forwarded message ----------
> From: Francesco Pietra <>
> 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 <>,
> On Thu, Mar 8, 2012 at 3:27 PM, francesco oteri
> <> 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 <> 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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Received on Fri Mar 09 2012 - 10:30:03 PST
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