[gmx-users] [HELP] Residue 'NI' not found in residue topology database , Vol 184, Issue 67

Edjan Silva edjan.silva at esenfar.ufal.br
Tue Aug 27 17:55:59 CEST 2019 

The only .rtp file is aminoacids.rtp. So should I add NI topological
descriptions to this file?

Em seg, 26 de ago de 2019 às 14:16, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> escreveu:

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> Today's Topics:
>
>    1. Gromacs 2019.3 compilation with GPU support (Prithwish Nandi)
>    2. [HELP] Residue 'NI' not found in residue topology database
>       (Edjan Silva)
>    3. Re: Gromacs 2019.3 compilation with GPU support (Mark Abraham)
>    4. Re: [HELP] Residue 'NI' not found in residue topology
>       database (Justin Lemkul)
>    5. Re: (no subject) (Navneet Kumar Singh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 26 Aug 2019 15:50:35 +0000
> From: Prithwish Nandi <prithwish.nandi at ichec.ie>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Gromacs 2019.3 compilation with GPU support
> Message-ID:
>         <
> 0102016cce9f3410-fb8dc07f-2f6a-480d-ba4c-6371bb5d00a3-000000 at eu-west-1.amazonses.com
> >
>
> Content-Type: text/plain;       charset=utf-8
>
> Hi,
> I am trying to compile Gromacs-2019.3 at our HPC cluster. I successfully
> compiled the single and double precision versions, but it?s producing error
> for GPU support. (The error message is pasted below)
>
> I am using Intel/2018 update 4 and CUDA/10.0. The base gcc version is
> 4.8.5. Using MKL as the FFTW lib and mliicc as the C compiler, and mpiicpc
> as the CXX compiler.
>
> The error I am getting is given below.
>
> Do you have any clue for this?
>
> Thanks, //PN
>
> The error message:
>
>   Error generating file
>
> /xxx/xxx/gromacs/intel/2019.3/kay/gromacs-2019.3/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o
>
>
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o]
> Error 1
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error:
> identifier "_mm_set1_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error:
> identifier "_mm_set1_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error:
> identifier "_mm_set_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> identifier "_mm_set_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> identifier "_mm_and_si128" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error:
> identifier "_mm_set_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error:
> identifier "_mm_or_si128" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error:
> identifier "_mm_sub_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error:
> identifier "_mm_mul_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> identifier "_mm_hadd_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> identifier "_mm_cvtsd_f64" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> identifier "_mm_mul_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> identifier "_mm_add_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error:
> identifier "_mm_storeu_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error:
> identifier "_mm_set1_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error:
> identifier "_mm_set1_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error:
> identifier "_mm_set_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> identifier "_mm_set_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> identifier "_mm_and_si128" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error:
> identifier "_mm_set_epi64x" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error:
> identifier "_mm_or_si128" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error:
> identifier "_mm_sub_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error:
> identifier "_mm_mul_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> identifier "_mm_hadd_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> identifier "_mm_cvtsd_f64" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> identifier "_mm_mul_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> identifier "_mm_add_pd" is undefined
>
> /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error:
> identifier "_mm_storeu_pd" is undefined
>
> 14 errors detected in the compilation of
> "/localscratch/397189/tmpxft_00006280_00000000-6_gpubonded-impl.cpp4.ii".
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 26 Aug 2019 13:04:27 -0300
> From: Edjan Silva <edjan.silva at esenfar.ufal.br>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] [HELP] Residue 'NI' not found in residue topology
>         database
> Message-ID:
>         <
> CAPf4pybnPh9-TUv39Z-Nsd5zWZFxGCiUkLSKt0tFiRFxjL1rqg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear users,
>
> I am trying to perform a simulation with a protein which contains two
> nickel atoms in the active site.
>
> When using the pdb2gmx command the following error appears:
>
> 'NI' not found in residue topology database
>
> I have edited the ions.itp file in the force field directory used (opls)
> but the same error still appears.
>
> Best regards,
>
> Edjan.
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 26 Aug 2019 18:38:28 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Gromacs 2019.3 compilation with GPU support
> Message-ID:
>         <
> CAMNuMAQDjsyVLm4Bv-DvQqLEh1xf1HWj+rgrAmgzTjMarHFJsQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> All versions of icc requires a standard library from an installation of
> gcc. There are various dependencies between them, and your system admins
> should have an idea which one is known to work well in your case. If you
> need to help the GROMACS build find the right one, do check out the GROMACS
> install guide for how to direct a particular gcc to be used with icc. I
> would suggest nothing earlier than gcc 5.
>
> Mark
>
>
> On Mon, 26 Aug 2019 at 17:51, Prithwish Nandi <prithwish.nandi at ichec.ie>
> wrote:
>
> > Hi,
> > I am trying to compile Gromacs-2019.3 at our HPC cluster. I successfully
> > compiled the single and double precision versions, but it?s producing
> error
> > for GPU support. (The error message is pasted below)
> >
> > I am using Intel/2018 update 4 and CUDA/10.0. The base gcc version is
> > 4.8.5. Using MKL as the FFTW lib and mliicc as the C compiler, and
> mpiicpc
> > as the CXX compiler.
> >
> > The error I am getting is given below.
> >
> > Do you have any clue for this?
> >
> > Thanks, //PN
> >
> > The error message:
> >
> >   Error generating file
> >
> >
> /xxx/xxx/gromacs/intel/2019.3/kay/gromacs-2019.3/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o
> >
> >
> > make[2]: ***
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o]
> > Error 1
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error:
> > identifier "_mm_set1_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error:
> > identifier "_mm_set1_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error:
> > identifier "_mm_set_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> > identifier "_mm_set_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> > identifier "_mm_and_si128" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error:
> > identifier "_mm_set_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error:
> > identifier "_mm_or_si128" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error:
> > identifier "_mm_sub_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error:
> > identifier "_mm_mul_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> > identifier "_mm_hadd_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> > identifier "_mm_cvtsd_f64" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> > identifier "_mm_mul_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> > identifier "_mm_add_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error:
> > identifier "_mm_storeu_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error:
> > identifier "_mm_set1_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error:
> > identifier "_mm_set1_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error:
> > identifier "_mm_set_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> > identifier "_mm_set_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error:
> > identifier "_mm_and_si128" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error:
> > identifier "_mm_set_epi64x" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error:
> > identifier "_mm_or_si128" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error:
> > identifier "_mm_sub_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error:
> > identifier "_mm_mul_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> > identifier "_mm_hadd_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error:
> > identifier "_mm_cvtsd_f64" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> > identifier "_mm_mul_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error:
> > identifier "_mm_add_pd" is undefined
> >
> > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error:
> > identifier "_mm_storeu_pd" is undefined
> >
> > 14 errors detected in the compilation of
> > "/localscratch/397189/tmpxft_00006280_00000000-6_gpubonded-impl.cpp4.ii".
> >
> >
> >
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 26 Aug 2019 13:03:49 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] [HELP] Residue 'NI' not found in residue
>         topology database
> Message-ID: <3668fd06-bd5e-a176-8695-428bff11e650 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/26/19 12:04 PM, Edjan Silva wrote:
> > Dear users,
> >
> > I am trying to perform a simulation with a protein which contains two
> > nickel atoms in the active site.
> >
> > When using the pdb2gmx command the following error appears:
> >
> > 'NI' not found in residue topology database
> >
> > I have edited the ions.itp file in the force field directory used (opls)
> > but the same error still appears.
>
> pdb2gmx does not read .itp files, it reads .rtp files. You need to add a
> residue definition there.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 26 Aug 2019 22:44:32 +0530
> From: Navneet Kumar Singh <navneetcdl at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
> Message-ID:
>         <CAOvdM4Uw=
> yPN1gFQK+H4WHrj1vozny67swEtfQGBbEYfgRi4sA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Do I have to add vsite3 information from unk.itp to system.top files?
>
> -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
>
> On Mon, 26 Aug 2019, 00:58 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> > > Yeah! I have read that.
> > >
> > > uses -maxwarn 1 to produce .tpr file using grompp command as mentioned
> in
> >
> > Since you are getting an error rather than a warning, that means you are
> > not using GROMACS 2016.x, as the instructions I pointed to you say.
> >
> > If you want to use a different GROMACS version, you have to change the
> > topology. Again see the link I provided for a description of what to do.
> >
> > -Justin
> >
> > > python script cgenff_charmm2gmx_py2.py
> > >
> > > output of cgenff_charmm2gmx_py2.py
> > >
> >
> _____________________________________________________________________________________________________________________________________________________________
> > >
> > > NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> > Mar
> > > 26 2019, 10:00:46)
> > > [GCC 5.4.0 20160609]
> > >
> > > NOTE 2: Please be sure to use the same version of CGenFF in your
> > > simulations that was used during parameter generation:
> > > --Version of CGenFF detected in  unk.str : 4.0
> > > --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> 4.0
> > >
> > > NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> > > parameters that are already in CGenFF' option when uploading a molecule
> > > into CGenFF.
> > >
> > > NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> > This
> > > is not a problem, just FYI!
> > >
> > > ============ DONE ============
> > > Conversion complete.
> > > The molecule topology has been written to unk.itp
> > > Additional parameters needed by the molecule are written to unk.prm,
> > which
> > > needs to be included in the system .top
> > >
> > > PLEASE NOTE: lone pair construction requires duplicate host atom
> numbers,
> > > which will make grompp complain
> > > To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> > check
> > >
> >
> ________________________________________________________________________________________________________________________________________________________________
> > >
> > > After that I am using same -maxwarn 1 but still, it's giving error. It
> > may
> > > be some silly mistake please let me know.
> > >
> > >
> > > On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > >>
> > >> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> > >>> Thank You Sir!
> > >>>
> > >>> Attached file can be downloaded from following link.
> > >>>
> > >>> https://fil.email/OR7Nsh0f
> > >>> <https://fil.email/OR7Nsh0f?&showconfirmation=true>
> > >>> ____________________________________________________________________
> > >>> Error
> > >>>
> > >>> ERROR 1 [file unk.itp, line 497]:
> > >>>     Duplicate atom index (23) in virtual_sites3
> > >>> ___________________________________________________________________
> > >>>
> > >>> It support lone pair construction for halogens only. Please suggest
> > some
> > >>> alternatives.
> > >> The link I provided before describes what you need to do. Please
> consult
> > >> that information.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==================================================
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Assistant Professor
> > >> Office: 301 Fralin Hall
> > >> Lab: 303 Engel Hall
> > >>
> > >> Virginia Tech Department of Biochemistry
> > >> 340 West Campus Dr.
> > >> Blacksburg, VA 24061
> > >>
> > >> jalemkul at vt.edu | (540) 231-3129
> > >> http://www.thelemkullab.com
> > >>
> > >> ==================================================
> > >>
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-request at gromacs.org.
> > >>
> > >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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