From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Fri Oct 30 2009 - 17:02:48 CDT
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
> >
> > ------------------------------------------------------------------------
> > Windows Live: Make it easier for your friends to see what you’re up to
> > on Facebook.
> > <http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009>
>
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<br>Hello Peter<br><br>I try to apply patches manually but I got the following message: "Resid missing from patch target 14ba. Molecule destroyed by fatal error."<br>Regarding coordinates you are right about the warnings:<br>First there is "Open coordinate file xxxx-pdb for writing.<br>Read PDB CONECT records .....<br>Warning I couldn't find the original pdb to assign connectivity. Using autogenerated connectivity only."<br>But the resulting xxx-temp.xbgf file produced at this stage is still containing th required coordinates<br>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<br>"Warning: Failed to set coordinates for atom XX" where atom naming from the initial PDB is being used.<br>Is there anything I can do about this ?<br><br>Many thanks and kind regards<br>Vlad<br> <br>> Date: Thu, 29 Oct 2009 20:31:00 -0400<br>> From: petefred_at_ks.uiuc.edu<br>> To: vchindea_at_hotmail.com<br>> CC: namd-l_at_ks.uiuc.edu<br>> Subject: Re: namd-l: issues with AutoPSF for a cyclodextrin<br>> <br>> Hi Vlad,<br>> autopsf does not do anything to automatically detect when arbitrary<br>> bonding patches should be applied (which would really be a complex<br>> problem). You can either apply the patches that you need manually<br>> through the patch dialogue, or alter the topology to make those bonds<br>> part of the residue definition.<br>> More information would be required to determine the lack of coordinates<br>> -- were there any warnings or errors while psfgen was running?<br>> Best,<br>> Peter<br>> <br>> CHINDEA Vlad wrote:<br>> > Dear NAMD users<br>> ><br>> > I am trying to build the PSF of a cyclodextrin starting from an X-ray<br>> > diffraction PDB with a bit of manual adjustment done (file attached).<br>> > I have used topology files top_all22_sugar.inp and/or<br>> > top_all36_carb.inp. When applying AutoPSF the 10 interconnected<br>> > glucose residues were replaced by 10 independent glucose molecules in<br>> > the resulting PSF and PSB although patches for alpha glycosidic bond<br>> > are available at least in top_all36_carb.inp. Also the PDB contains<br>> > only blank coordinates. What would be the reason and what can I do<br>> > about it ?<br>> ><br>> > I would like to mention that I have changed the name of the glucose<br>> > residue from AGLC to AGL in topology and PDB file as according to my<br>> > knowledge (PDB specs 3.20) residue names should have only 3 characters.<br>> ><br>> > Many thanks for your support<br>> > Best wishes<br>> > Vlad<br>> ><br>> > ------------------------------------------------------------------------<br>> > Windows Live: Make it easier for your friends to see what you’re up to<br>> > on Facebook.<br>> > <http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009>
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