Fwd: ANGLE PARAMETERS FOR NH3 HC NH3

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 27 2015 - 11:19:48 CDT

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:

*Info: SUMMARY OF PARAMETERS:Info: 191 BONDSInfo: 488 ANGLESInfo: 601
DIHEDRALInfo: 47 IMPROPERInfo: 6 CROSSTERMInfo: 125 VDWInfo: 0
VDW_PAIRSInfo: 0 NBTHOLE_PAIRSFATAL 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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