VMD-L Mailing List

From: hodak_at_chips.ncsu.edu
Date: Tue Nov 22 2005 - 05:13:43 CST

I stripped all hydrogens from my starting dipeptide (HG) but the problem
is still there (namd still complains). I cannot spot the atoms that are
close or identitical, but 27th atom has 0,0,0 coordinates. I am attachaing
my starting pdb file and also the script I am using.

Thanks,
        Miro

On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:

> okay... I have one more question... Is your starting protein WITHOUT hydrogen atoms? if yes, remove all of them prior building your psf and pdb files. You can also check that the structure of your protein is correct (e.g., that you don't have duplicated atoms).
>
> Try to do that and tell me if you see something weird. You can also send me your pdb file and I can check it.
>
> Cheers,
> Michel
>
> ________________________________
>
> From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> Sent: Tue 11/22/2005 4:40 AM
> To: Michel Espinoza-Fonseca
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: Uncharged terminal ends?
>
>
>
> It seems that I have one more issue with generated pdb file. When I run
> namd I get:
> Warning: Not all atoms have unique coordinates.
>
> Inspecting generated pdb file, my CA on G has two hydrogen that are very
> close (and CA actually has 5 bonds):
>
> ATOM 27 HA GLY 3 4.826 -0.964 -1.247 1.00 0.00 PROT H
> ATOM 36 HA2 GLY 3 4.806 -0.987 -1.255 0.00 0.00 PROT H
>
> Please note that 36 is my last atom.
> It seems like problem with psfgen's guessing of coordinates (guesscoord).
>
> What can I do to avoid this problem?
>
> Thanks,
> Miro
>
> On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
>
> > "auto none" automatically generates angles and dihedrals based on bonds, since the topology file don't list angles and dihedrals. This is specially needed when you apply patches on your protein (such as ACE or CT1) or with water.
> >
> > Hope it is clear,
> > Michel
> >
> > ________________________________
> >
> > From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> > Sent: Tue 11/22/2005 4:16 AM
> > To: Michel Espinoza-Fonseca
> > Cc: vmd-l_at_ks.uiuc.edu
> > Subject: RE: vmd-l: Uncharged terminal ends?
> >
> >
> >
> > With this I am namd simulation will start. Now what is does "auto none"
> > actually do?
> >
> > Thanks,
> > Miro
> >
> > On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
> >
> > > mmmm... try to rebuild your system using
> > >
> > > first ACE
> > > last CT1
> > > auto none
> > >
> > > and then see if it works...
> > >
> > > ________________________________
> > >
> > > From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> > > Sent: Tue 11/22/2005 4:00 AM
> > > To: Michel Espinoza-Fonseca
> > > Cc: vmd-l_at_ks.uiuc.edu
> > > Subject: RE: vmd-l: Uncharged terminal ends?
> > >
> > >
> > >
> > > I cannot minimize the system (at least not with namd), since I get that error
> > > about HB CT1 HB angle parameters when I try to run namd with my system.
> > >
> > > On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
> > >
> > > > That's weird... Are you minimizing your system first ? Usually I get the same thing you described (multiple bonds on the ACE or NME terminals), but you can easily solve this problem by subjecting your system to a short (~1000 steps) minimization.
> > > >
> > > > After that you should't have any problem.
> > > >
> > > > Hope it helps.
> > > >
> > > > Michel
> > > >
> > > > ________________________________
> > > >
> > > > From: owner-vmd-l_at_ks.uiuc.edu on behalf of hodak_at_chips.ncsu.edu
> > > > Sent: Tue 11/22/2005 3:18 AM
> > > > To: Justin Gullingsrud
> > > > Cc: vmd-l_at_ks.uiuc.edu
> > > > Subject: Re: vmd-l: Uncharged terminal ends?
> > > >
> > > >
> > > >
> > > > This helped a lot. I decided that I want acetylated N-terminus and
> > > > methylated C-terminus. Using
> > > >
> > > > first ACE
> > > > last CT1
> > > >
> > > > I can get the ends I want, although vmd shows extra bonds that those added
> > > > groups have carbons connected to N or C. I am not sure if this is a
> > > > problem or not.
> > > > I went ahead and used generated psf and pdb files as input for namd
> > > > simulation, but I get the following error:
> > > >
> > > > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> > > > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > > > Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> > > >
> > > > Charm++ fatal error:
> > > > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> > > >
> > > > The problem seems to be the C-terminal end, omitting "last CT1" namd
> > > > simulation runs without problems.
> > > >
> > > > Any idea what the problem is and how it can be solved?
> > > >
> > > > Thanks,
> > > > Miro
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, 21 Nov 2005, Justin Gullingsrud wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You probably want an acetylated N terminus, then, which you can get by
> > > > > specifying "first ACE". I'm not sure what kind of C terminus you're
> > > > > looking for, but check out the PRES patches in the topology file to
> > > > > see what's available.
> > > > >
> > > > > Hope this helps,
> > > > > Justin
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
> >
>
>
>

  • chemical/x-pdb attachment: HG3.pdb