Francesco,
> I forgot to ask why VMD does not show the existing (according to leap and
> parmed.py) bonds between the protein backbone and the active center. In
> contrast, all internal bonds in the active center are shown in VMD (they
> where raised from a mol2 file with CONECT).
vmd toto.mol2
and
vmd toto.parm7 toto.rst7
should give you the same results if the mol2 file is used (LEaP) to
generate the parm7/rst files
on the contrary with
vmd toto.pdb
only bonds (based on vmd internal algo.) found by vmd will be created;
i.e. only bonds below vmd internal thresholds will be found.
we already discussed about that...
regards, Francois
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret.gmail.com>
> Date: Mon, Jan 5, 2015 at 9:37 AM
> Subject: Re: [AMBER] Checking bonds commanded with leap
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> xparmed.py my.parm7
>
> allowed to just clicking on "printBonds". As a mask, after some trial and
> error, I used
>
>
> ":protein-residue","active-center-residue"
>
>
> As far as I can understand, the output bond strength is the one I set in
> the parameters, while Rmin does not correspond to the actual interatomic
> distances (particularly as to the couple of too long bonds I have, 3 and
> 4A). Rather, it should correspond to just Rmin for such a bond. I was
> surprised that it outputted Rmin for also iron-other_element bonds, most of
> which are still to be assessed (I gave grossly estimated values, just to
> see whether leap works with my files).
>
> To the latter concern, has anyone developed and independent (independent
> from tools on AmberTools) working out of the Cartesian matrix for complex
> cases dealt with "ab initio" as in my case?
>
> thanks
> francesco
>
> On Sun, Jan 4, 2015 at 5:35 PM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
>> Hello,
>>
>> Parmed (parmed.py) could help you with the "PrintBonds" command.
>>
>> Gerald.
>>
>> On 01/03/2015 07:25 PM, Francesco Pietra wrote:
>> > Sorry for asking what will be common knowledge: where to check for bonds
>> > formed that were commanded to leap (similarly to what is shown in psf
>> > charmm files). I have both regular distances and too long distance for
>> > regular bonds (between enzyme backbone and active center), none detected
>> by
>> > loading parm7/rst7 to vmd, while indicated on leap log.
>> > thanks
>> > francesco pietra
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jan 05 2015 - 23:30:02 PST
