RE: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Oct 28 2015 - 20:36:08 CDT

If it helps, as it happens I was just looking through the latest CHARMM-36 release the other day. In stream/prot/toppar_all36_prot_modify_res.str you’ll find patches to covalently link cysteine and histidine residues to zinc (look for PRES entries CSN, ZN_C, ZNHD and ZNHE).

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Francesco Pietra
Sent: Wednesday, 28 October 2015 4:34 AM
To: Josh Vermaas
Cc: NAMD
Subject: Re: namd-l: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3

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<mailto: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<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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