From: Angelo Rossi (angelo.raymond.rossi_at_gmail.com)
Date: Wed Apr 26 2017 - 11:00:24 CDT
Dear Marcelo:
You were absolutely correct!
When I use the tcl script that helps in setting up the QM region, I
obtained a pdb file that worked.
The problem wasn't related to extended psf files at all.
Thanks so much for your quick response.
Kind regards,
Angelo
On Wed, Apr 26, 2017 at 10:32 AM, Marcelo C. R. Melo <melomcr_at_gmail.com>
wrote:
> 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 <(217)%20244-5983>
>
> 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/noa
>> rch/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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