VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Apr 17 2019 - 16:59:41 CDT

Hi Pablo,

 

Thank you for you contact. In short no, it is not possible to disable this auto-assignment in QwikMD, although it is on my to-do list.

 

Best

 

João

 

 

……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois

http://www.ks.uiuc.edu/~jribeiro/

jribeiro_at_illinois.edu

+1 (217) 3005851

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Pablo Alfonso Madero Ayala <pmadero_at_uabc.edu.mx>
Date: Wednesday, April 17, 2019 at 4:46 PM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Problem with QwikMD automatic NTER patch

 

Hello,

 

I am trying to simulate a truncated N terminal protein, for this reason I am applying the ACE patch to the amino terminus. The problem is that QwikMD automatically applies the NTER patch, so the final structure has two patches in the first residue

 

PSF CMAP

 

      20 !NTITLE

 REMARKS original generated structure x-plor psf file

 REMARKS 5 patches were applied to the molecule.

 REMARKS topology XP1_formatted_autopsf-temp.top

 REMARKS topology C:/Program

 REMARKS topology C:/Program Files (x86)/University of Illinois/VMD/plugins/noarch/tcl/readcharmmtop1.2/toppar_water_ions_namd.str

 REMARKS segment XP1 { first NTER; last CTER; auto angles dihedrals }

 REMARKS segment WT1 { first NONE; last NONE; auto none }

 REMARKS segment WT2 { first NONE; last NONE; auto none }

 REMARKS segment WT3 { first NONE; last NONE; auto none }

 REMARKS segment WT4 { first NONE; last NONE; auto none }

 REMARKS segment WT5 { first NONE; last NONE; auto none }

 REMARKS segment WT6 { first NONE; last NONE; auto none }

 REMARKS segment WT7 { first NONE; last NONE; auto none }

 REMARKS segment WT8 { first NONE; last NONE; auto none }

 REMARKS segment ION { first NONE; last NONE; auto none }

 REMARKS patch CTER XP1:242

 REMARKS patch NTER XP1:7

 REMARKS patch SERD XP1:188

 REMARKS patch ACE XP1:7

 REMARKS patch DISU XP1:59 XP1:240

 

   51590 !NATOM

       1 XP1 7 ALA CAY CT3 -0.270000 12.0110 0

       2 XP1 7 ALA HY1 HA3 0.090000 1.0080 0

       3 XP1 7 ALA HY2 HA3 0.090000 1.0080 0

       4 XP1 7 ALA HY3 HA3 0.090000 1.0080 0

       5 XP1 7 ALA CY C 0.510000 12.0110 0

       6 XP1 7 ALA OY O -0.510000 15.9990 0

       7 XP1 7 ALA N NH3 -0.300000 14.0070 0

       8 XP1 7 ALA HT1 HC 0.330000 1.0080 0

       9 XP1 7 ALA HT2 HC 0.330000 1.0080 0

      10 XP1 7 ALA HT3 HC 0.330000 1.0080 0

      11 XP1 7 ALA CA CT1 0.210000 12.0110 0

      12 XP1 7 ALA HA HB1 0.100000 1.0080 0

      13 XP1 7 ALA CB CT3 -0.270000 12.0110 0

      14 XP1 7 ALA HB1 HA3 0.090000 1.0080 0

      15 XP1 7 ALA HB2 HA3 0.090000 1.0080 0

      16 XP1 7 ALA HB3 HA3 0.090000 1.0080 0

      17 XP1 7 ALA C C 0.510000 12.0110 0

      18 XP1 7 ALA O O -0.510000 15.9990 0

      19 XP1 8 LEU N NH1 -0.470000 14.0070 0

      20 XP1 8 LEU HN H 0.310000 1.0080 0

      21 XP1 8 LEU CA CT1 0.070000 12.0110 0

      22 XP1 8 LEU HA HB1 0.090000 1.0080 0

      23 XP1 8 LEU CB CT2 -0.180000 12.0110 0

      24 XP1 8 LEU HB1 HA2 0.090000 1.0080 0

      25 XP1 8 LEU HB2 HA2 0.090000 1.0080 0

      26 XP1 8 LEU CG CT1 -0.090000 12.0110 0

      27 XP1 8 LEU HG HA1 0.090000 1.0080 0

      28 XP1 8 LEU CD1 CT3 -0.270000 12.0110 0

      29 XP1 8 LEU HD11 HA3 0.090000 1.0080 0

      30 XP1 8 LEU HD12 HA3 0.090000 1.0080 0

      31 XP1 8 LEU HD13 HA3 0.090000 1.0080 0

      32 XP1 8 LEU CD2 CT3 -0.270000 12.0110 0

      33 XP1 8 LEU HD21 HA3 0.090000 1.0080 0

      34 XP1 8 LEU HD22 HA3 0.090000 1.0080 0

      35 XP1 8 LEU HD23 HA3 0.090000 1.0080 0

      36 XP1 8 LEU C C 0.510000 12.0110 0

      37 XP1 8 LEU O O -0.510000 15.9990 0

 

As you can see, this results in a NH3 terminal with an additional acetyl group which produces the following error at the beginning of the simulation:

 

      FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 5 7)

 

I would like to know if there is any way to prevent the automatic application of the NTER patch in QwikMD.

 

 

*********************************************************************************
Pablo A. Madero,

Master in Science student

E-Mail: pmadero_at_uabc.edu.mx
Autonomous University of Baja California

Faculty of chemical sciences and engineering

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