This is because I put three TER records to get rid of three ca 50A long bonds
that just crossed the opening of the pore protein. Don't ask me why such long
bonds were there, it was done by o.p. removing most helices except those of the
pore. At any event the gross shape of the pore is still quite similar to the
experimental one. Curiously, the long bonds were advertised by Chimera, not by
VMD, although they prevented going on with dock.
Now I want to carry out docking with natural products treated by Antechamber,
and MD with Amber9, and back docking. Perhaps I started along a steep way as a
first approach to the biopolymer. I still have to see what capping means in
this context and if it may turn useful here.
Thanks
francesco
--- Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> it seems fine, just telling you that you have 4 separate chains
> with N and C termini. If that's not what you want, or if you want
> to put capping groups on them, then you need to change it.
>
> On 10/29/07, Francesco Pietra <chiendarret.yahoo.com> wrote:
> > I had a lot of problems in fixing a large protein model. The last step was
> > using leal (leaprc.ff99SB in Amber9). Heavy atoms were added where I had
> set
> > TER records, res 111, 222, 333, and at res 444, besides 38 H/lone pairs.
> Both
> > prmtop and inpcrd could be saved (and opened correctly with VMD or
> Chimera).
> > The total charge is 24.000000. Not neutralized, not solvated, not tried to
> > minimize yet.
> >
> > The last part of leap.log reads:
> >
> > (Residues lacking connect 0/ connect 1 -
> > These don't have chain types marked:
> > res total affected
> > CTHR 4
> > NSER 4
> >
> > Is that of concern or can I go on with these prmtop inpcrd?
> >
> > Thanks
> > francesco pietra
> >
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Received on Wed Oct 31 2007 - 06:07:35 PDT
