From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Oct 27 2015 - 11:24:47 CDT
What does the rest of the generate statement look like? There is a
default NTER and CTER applied to protein segments, so you may have
double patched something, which ends poorly.
-Josh
On 10/27/2015 11:19 AM, Francesco Pietra wrote:
> As there two REMARKS in the psf file about NTER, please notice that in
> the text-mode gen for vmd (calling psfgen) I explicitly asked
>
> patch NTER PRA:2
>
> regenerate angles dihedrals
>
>
> Is that a redundancy that created the problem?
>
> thanks
> fp
>
> ---------- Forwarded message ----------
> From: *Francesco Pietra* <chiendarret_at_gmail.com
> <mailto:chiendarret_at_gmail.com>>
> Date: Tue, Oct 27, 2015 at 5:12 PM
> Subject: ANGLE PARAMETERS FOR NH3 HC NH3
> To: NAMD <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>>
>
>
> Hello:
> While trying to minimize a metalloproteinunder charmm27, with ALA
> first residue (nr 2), the log reports:
>
> *Info: SUMMARY OF PARAMETERS:
> Info: 191 BONDS
> Info: 488 ANGLES
> Info: 601 DIHEDRAL
> Info: 47 IMPROPER
> Info: 6 CROSSTERM
> Info: 125 VDW
> Info: 0 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 (ATOMS 1 4 1)
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3
> (ATOMS 1 4 1)*
>
>
> The relevant part of the psf file shows that the first residue was patched
>
>
> *REMARKS segment ION { first NONE; last NONE; auto angles dihedrals }
> REMARKS defaultpatch NTER PRA:2
> REMARKS patch CTER PRA:131
> REMARKS patch NTER PRA:2
>
> 34366 !NATOM
> 1 PRA 2 ALA N NH3 -0.300000 14.0070 0
> 2 PRA 2 ALA HT1 HC 0.330000 1.0080 0
> 3 PRA 2 ALA HT2 HC 0.330000 1.0080 0
> 4 PRA 2 ALA HT3 HC 0.330000 1.0080 0
> 5 PRA 2 ALA CA CT1 0.210000 12.0110 0
> *
> Apparently the system does not complain about the metal center. I
> never met that error with patched NTER. Thanks for advice
>
> francesco pietra
>
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