AMBER Archive (2007)

Subject: Re: AMBER: Getting prmtop and inpcrd

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Oct 29 2007 - 09:47:33 CST

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_at_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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