Re: FW: issues with AutoPSF for a cyclodextrin - addendum

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Oct 30 2009 - 19:20:03 CDT

Hi Vlad,
one must **always** use the same atom names as are in the topology file,
so it is not surprising that you ran into problems.
The reason that autopsf split your molecule into separate segments is
that it didn't recognize it as a polymer (I only have code in there to
recognize proteins or nucleic acids). You should be able to use the
chains interface to delete the automatically generated ones and add one
that contains all of the residues. The best solution if you're going to
do this a lot is to add the bonds to the topology file.
Best,
Peter

CHINDEA Vlad wrote:
> Hi Peter
>
> In the mean time I have solved it by using a different input PDB with
> proper atom names for top file. Patches were added manually (BTW
> molecule was splitted by AutoPSF as one segment for each residue,
> which looks a bit strange to me).
>
> Many thanks for your time
> Vlad
>
> ------------------------------------------------------------------------
> From: vchindea_at_hotmail.com
> To: namd-l_at_ks.uiuc.edu
> Subject: RE: namd-l: issues with AutoPSF for a cyclodextrin
> Date: Sat, 31 Oct 2009 00:02:48 +0200
>
>
> Hello Peter
>
> I try to apply patches manually but I got the following message:
> "Resid missing from patch target 14ba. Molecule destroyed by fatal error."
> Regarding coordinates you are right about the warnings:
> First there is "Open coordinate file xxxx-pdb for writing.
> Read PDB CONECT records .....
> Warning I couldn't find the original pdb to assign connectivity. Using
> autogenerated connectivity only."
> But the resulting xxx-temp.xbgf file produced at this stage is still
> containing th required coordinates
> And then after pressing "Create chain" residues from the original PDB
> are being replaced by non-interconnected residues from the topology
> file. With this also atom names are changed to the names from topology
> and hence subsequently there are a lot of
> "Warning: Failed to set coordinates for atom XX" where atom naming
> from the initial PDB is being used.
> Is there anything I can do about this ?
>
> Many thanks and kind regards
> Vlad
>
> > Date: Thu, 29 Oct 2009 20:31:00 -0400
> > From: petefred_at_ks.uiuc.edu
> > To: vchindea_at_hotmail.com
> > CC: namd-l_at_ks.uiuc.edu
> > Subject: Re: namd-l: issues with AutoPSF for a cyclodextrin
> >
> > Hi Vlad,
> > autopsf does not do anything to automatically detect when arbitrary
> > bonding patches should be applied (which would really be a complex
> > problem). You can either apply the patches that you need manually
> > through the patch dialogue, or alter the topology to make those bonds
> > part of the residue definition.
> > More information would be required to determine the lack of coordinates
> > -- were there any warnings or errors while psfgen was running?
> > Best,
> > Peter
> >
> > CHINDEA Vlad wrote:
> > > Dear NAMD users
> > >
> > > I am trying to build the PSF of a cyclodextrin starting from an X-ray
> > > diffraction PDB with a bit of manual adjustment done (file attached).
> > > I have used topology files top_all22_sugar.inp and/or
> > > top_all36_carb.inp. When applying AutoPSF the 10 interconnected
> > > glucose residues were replaced by 10 independent glucose molecules in
> > > the resulting PSF and PSB although patches for alpha glycosidic bond
> > > are available at least in top_all36_carb.inp. Also the PDB contains
> > > only blank coordinates. What would be the reason and what can I do
> > > about it ?
> > >
> > > I would like to mention that I have changed the name of the glucose
> > > residue from AGLC to AGL in topology and PDB file as according to my
> > > knowledge (PDB specs 3.20) residue names should have only 3
> characters.
> > >
> > > Many thanks for your support
> > > Best wishes
> > > Vlad
> > >
> > >
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