From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 27 2015 - 13:33:59 CDT
Hi Josh:
Yes, it was the redundant patching NTER that created the problem
Now problems with the transition metal center, but this another (bigger)
story
thanks
francesco
On Tue, Oct 27, 2015 at 5:24 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> 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>
> Date: Tue, Oct 27, 2015 at 5:12 PM
> Subject: ANGLE PARAMETERS FOR NH3 HC NH3
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Hello:
> While trying to minimize a metalloproteinunder charmm27, with ALA first
> residue (nr 2), the log reports:
>
>
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> *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
>
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> *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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