From: Angelo Rossi (angelo.raymond.rossi_at_gmail.com)
Date: Wed Apr 26 2017 - 08:06:03 CDT
Hello:
I wanted to try out the NAMD QM/MM interface with a simple problem
involving the solvation of acetone. The QM component is acetone, and the
MM component involves the surrounding H2O molecules.
But, the acetone molecule requires the
*top_all36_cgenff.rtf/par_all36_cgenff.prm
*parameter set, employing extended characters for the file types, e.g.
HGAAM0, etc.
I believe that this requires the use of an extended psf file.
When I used an extended psf file (See below.), I received the following
error with NAMD:
[
*anr11010_at_cn01
acetone]$/shared/chem5326/NAMD_2.12_Linux-x86_64-multicore/namd2
config.ORCA.namd >config.ORCA.log[file orca_main/maininp2.cpp, line 257]:
Element name/number, dummy atom or point charge expected in COORDS ATOM-NO
1------------- Processor 0 Exiting: Called CmiAbort ------------Reason:
FATAL ERROR: Error running command for QM forces calculation.Charm++ fatal
error:FATAL ERROR: Error running command for QM forces calculation.*I think
that this is related to the inability of the QM component of NAMD to read
an extended psf file, but I am not sure. Please see a comparison of the
original psf file in the Example1 directory and my psf file for solvated
acetone.
*Original psf file in Example 1 Directory=================================*
PSF CMAP
8 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology PolyAlaQMD_formatted_autopsf-temp.top
REMARKS topology /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.6/wat.top
REMARKS segment XP1 { first NTER; last CTER; auto angles dihedrals }
REMARKS segment WT1 { first NONE; last NONE; auto none }
REMARKS patch CTER XP1:9
REMARKS patch NTER XP1:2
2279 !NATOM
1 XP1 2 ALA N NH3 -0.300000 14.0070 0
2 XP1 2 ALA HT1 HC 0.330000 1.0080 0
3 XP1 2 ALA HT2 HC 0.330000 1.0080 0
4 XP1 2 ALA HT3 HC 0.330000 1.0080 0
5 XP1 2 ALA CA CT1 0.210000 12.0110 0
6 XP1 2 ALA HA HB1 0.100000 1.0080 0
7 XP1 2 ALA CB CT3 -0.270000 12.0110 0
8 XP1 2 ALA HB1 HA3 0.090000 1.0080 0
9 XP1 2 ALA HB2 HA3 0.090000 1.0080 0
10 XP1 2 ALA HB3 HA3 0.090000 1.0080 0
snip -------------- snip -----------------snip ----------------- snip
---------------------
*My psf for Solvated Acetone===========================*
PSF EXT
1 !NTITLE
REMARKS VMD-generated NAMD/X-Plor PSF structure file
964 !NATOM
1 ACO 1 ACO O1 OG2D3 -0.480000
15.9994 0
2 ACO 1 ACO C1 CG2O5 0.400000
12.0110 0
3 ACO 1 ACO C2 CG331 -0.230000
12.0110 0
4 ACO 1 ACO C3 CG331 -0.230000
12.0110 0
5 ACO 1 ACO H21 HGA3 0.090000
1.0080 0
6 ACO 1 ACO H22 HGA3 0.090000
1.0080 0
7 ACO 1 ACO H23 HGA3 0.090000
1.0080 0
8 ACO 1 ACO H31 HGA3 0.090000
1.0080 0
9 ACO 1 ACO H32 HGA3 0.090000
1.0080 0
10 ACO 1 ACO H33 HGA3 0.090000
1.0080 0
snip -------------- snip -----------------snip ----------------- snip
---------------------
Now the good news.
Recently, ORCA 4.0 was released, and I tried it with the sample data in the
Example1 directory. It worked flawlessly.
I hope you can help me resolve my problem above.
Thanks so much for your help with this.
Kind regards,
Angelo
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