Re: Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Wed Apr 26 2017 - 09:32:15 CDT

Hi Angelo.

Great to hear you are working with the QM/MM interface.

Could you provide the relevant files? (PDB, PSF, parameters, config file)
I don't want to rule anything out just yet, but the is no "QM-specific" PSF
reading code, so different PSF formats should not be an issue.

The first point I would investigate, however, could be related to the PSF.
Does the PDB file for your system have the "element" column?
The ORCA error seems to indicate that the element name was not written in
its input file, which could indicate NAMD didn't get that information from
the PDB file.
In the Example1 that you mentioned, there is a TCL script that helps
setting up the QM region, and one of the steps is the use of a VMD plugin
to set element names for each atom in the system. Maybe the different atom
types were not recognized by that plugin, and no "element" column was
written. Maybe for the simple system you are using, you could have prepared
the PDB file for QM/MM by hand, and not added that last element column?
In any case, if you could make the files available, we could double check
the error.

Best,
Marcelo

---
Marcelo Cardoso dos Reis Melo
PhD Candidate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu
+1 (217) 244-5983
On 26 April 2017 at 08:06, Angelo Rossi <angelo.raymond.rossi_at_gmail.com>
wrote:
> 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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