Re: [gmx-users] QMMM install on GMX5.1

[Sunil Pokharel]

.
On Oc
t 15, 2016 3:00 AM, "Xianchi Dong"  wrote:
> 0
> Hi all,
> Does anyone know how to install qmmm code like mopac to gmx5.1?
>
> Best,
> Xianchi
> --
> Gromacs Users mailing list
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Re: [gmx-users] QMMM install on GMX5.1 (Xianchi Dong)

[Andrew Guy]

Hi Xianchi,

A Google search of "domop_ gromacs" yields the following as the first hit:

https://redmine.gromacs.org/issues/1899

So it seems that this is a known bug, and unless anything has changed in
the last ~8 months, you may have a hard time getting QMMM to work with
recent versions of GROMACS.

I'm not well acquainted with this area, so happy for others to chime in
with other suggestions.

Andrew

On Mon, Oct 17, 2016 at 11:48 AM, Xianchi Dong <dongxian...@gmail.com>
wrote:

> Hi Andrew,
> Thanks for reply
>
> I tried to configure with cmake, the command I used is cmake ..
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DCMAKE_PREFIX_PATH=../../mopac_lib/
> -DCMAKE_INSTALL_PREFIX=~/Programs/Gromacs-5.1.2/ -DGMX_QMMM_MOPAC=on
>
> When I used make. It prompted with error msg:
>
> Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.1.2.0: undefined reference to `domop_'
> ../../lib/libgromacs.so.1.2.0: undefined reference to `domldt_'
> collect2: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> Best,
> Xianchi
>
> On Sun, Oct 16, 2016 at 8:37 PM, Andrew Guy <andrew@burnet.edu.au>
> wrote:
>
> > Hi Xianchi,
> >
> > It would be more helpful if you can provide a detailed description of
> what
> > failed when you tried to install QMMM. Just saying it failed doesn't give
> > people much insight into how to assist you.
> >
> > There are a myriad of possibilities, but without an actual error message
> to
> > go off, we're all in the dark here.
> >
> > Regards,
> >
> > Andrew
> >
> > On Mon, Oct 17, 2016 at 11:20 AM, Xianchi Dong <dongxian...@gmail.com>
> > wrote:
> >
> > > Hi Clinton,
> > > Thanks a lot for your reply. I tried but still failed.
> > > Would you like to say more about how to configure Gromacs 5.1.2 with
> > > CPPFLAGS, LIBS, and LDGFLAGS with cmake.
> > >
> > > Best,
> > > Xianchi
> > >
> > >
> > > > On Oct 15, 2016, at 12:52 PM, Clinton King <
> clintonkin...@chem.byu.edu
> > >
> > > wrote:
> > > >
> > > > Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
> > > >
> > > > You will also need to set the following variable at install time:
> > > >
> > > > -DGMX_QMMM_MOPAC=ON
> > > >
> > > > --
> > > > Clinton King
> > > > Graduate Student
> > > > Chemistry Department
> > > > Brigham Young University
> > > >
> > > >
> > > >>
> > > >>   1. QMMM install on GMX5.1 (Xianchi Dong)
> > > >>
> > > >>
> > > >> Message: 1
> > > >> Date: Fri, 14 Oct 2016 17:14:36 -0400
> > > >> From: Xianchi Dong <dongxian...@gmail.com>
> > > >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> > > >> Subject: [gmx-users] QMMM install on GMX5.1
> > > >> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com>
> > > >> Content-Type: text/plain; charset=us-ascii
> > > >>
> > > >> Hi all,
> > > >> Does anyone know how to install qmmm code like mopac to gmx5.1?
> > > >>
> > > >> Best,
> > > >> Xianchi
> > > >>
> > > >>
> > > >>
> > > > --
> > > > 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-requ...@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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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * 

Re: [gmx-users] QMMM install on GMX5.1 (Xianchi Dong)

[Xianchi Dong]

Hi Andrew,
Thanks for reply

I tried to configure with cmake, the command I used is cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_PREFIX_PATH=../../mopac_lib/
-DCMAKE_INSTALL_PREFIX=~/Programs/Gromacs-5.1.2/ -DGMX_QMMM_MOPAC=on

When I used make. It prompted with error msg:

Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to `domop_'
../../lib/libgromacs.so.1.2.0: undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

Best,
Xianchi

On Sun, Oct 16, 2016 at 8:37 PM, Andrew Guy <andrew@burnet.edu.au>
wrote:

> Hi Xianchi,
>
> It would be more helpful if you can provide a detailed description of what
> failed when you tried to install QMMM. Just saying it failed doesn't give
> people much insight into how to assist you.
>
> There are a myriad of possibilities, but without an actual error message to
> go off, we're all in the dark here.
>
> Regards,
>
> Andrew
>
> On Mon, Oct 17, 2016 at 11:20 AM, Xianchi Dong <dongxian...@gmail.com>
> wrote:
>
> > Hi Clinton,
> > Thanks a lot for your reply. I tried but still failed.
> > Would you like to say more about how to configure Gromacs 5.1.2 with
> > CPPFLAGS, LIBS, and LDGFLAGS with cmake.
> >
> > Best,
> > Xianchi
> >
> >
> > > On Oct 15, 2016, at 12:52 PM, Clinton King <clintonkin...@chem.byu.edu
> >
> > wrote:
> > >
> > > Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
> > >
> > > You will also need to set the following variable at install time:
> > >
> > > -DGMX_QMMM_MOPAC=ON
> > >
> > > --
> > > Clinton King
> > > Graduate Student
> > > Chemistry Department
> > > Brigham Young University
> > >
> > >
> > >>
> > >>   1. QMMM install on GMX5.1 (Xianchi Dong)
> > >>
> > >>
> > >> Message: 1
> > >> Date: Fri, 14 Oct 2016 17:14:36 -0400
> > >> From: Xianchi Dong <dongxian...@gmail.com>
> > >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> > >> Subject: [gmx-users] QMMM install on GMX5.1
> > >> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com>
> > >> Content-Type: text/plain; charset=us-ascii
> > >>
> > >> Hi all,
> > >> Does anyone know how to install qmmm code like mopac to gmx5.1?
> > >>
> > >> Best,
> > >> Xianchi
> > >>
> > >>
> > >>
> > > --
> > > 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-requ...@gromacs.org.
> > --
> > 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-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>
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Re: [gmx-users] QMMM install on GMX5.1 (Xianchi Dong)

[Andrew Guy]

Hi Xianchi,

It would be more helpful if you can provide a detailed description of what
failed when you tried to install QMMM. Just saying it failed doesn't give
people much insight into how to assist you.

There are a myriad of possibilities, but without an actual error message to
go off, we're all in the dark here.

Regards,

Andrew

On Mon, Oct 17, 2016 at 11:20 AM, Xianchi Dong <dongxian...@gmail.com>
wrote:

> Hi Clinton,
> Thanks a lot for your reply. I tried but still failed.
> Would you like to say more about how to configure Gromacs 5.1.2 with
> CPPFLAGS, LIBS, and LDGFLAGS with cmake.
>
> Best,
> Xianchi
>
>
> > On Oct 15, 2016, at 12:52 PM, Clinton King <clintonkin...@chem.byu.edu>
> wrote:
> >
> > Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
> >
> > You will also need to set the following variable at install time:
> >
> > -DGMX_QMMM_MOPAC=ON
> >
> > --
> > Clinton King
> > Graduate Student
> > Chemistry Department
> > Brigham Young University
> >
> >
> >>
> >>   1. QMMM install on GMX5.1 (Xianchi Dong)
> >>
> >>
> >> Message: 1
> >> Date: Fri, 14 Oct 2016 17:14:36 -0400
> >> From: Xianchi Dong <dongxian...@gmail.com>
> >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> >> Subject: [gmx-users] QMMM install on GMX5.1
> >> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com>
> >> Content-Type: text/plain; charset=us-ascii
> >>
> >> Hi all,
> >> Does anyone know how to install qmmm code like mopac to gmx5.1?
> >>
> >> Best,
> >> Xianchi
> >>
> >>
> >>
> > --
> > 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-requ...@gromacs.org.
> --
> 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-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] QMMM install on GMX5.1 (Xianchi Dong)

[Xianchi Dong]

Hi Clinton,
Thanks a lot for your reply. I tried but still failed. 
Would you like to say more about how to configure Gromacs 5.1.2 with CPPFLAGS, 
LIBS, and LDGFLAGS with cmake.

Best,
Xianchi


> On Oct 15, 2016, at 12:52 PM, Clinton King <clintonkin...@chem.byu.edu> wrote:
> 
> Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
> 
> You will also need to set the following variable at install time:
> 
> -DGMX_QMMM_MOPAC=ON
> 
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
> 
> 
>> 
>>   1. QMMM install on GMX5.1 (Xianchi Dong)
>> 
>> 
>> Message: 1
>> Date: Fri, 14 Oct 2016 17:14:36 -0400
>> From: Xianchi Dong <dongxian...@gmail.com>
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] QMMM install on GMX5.1
>> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com>
>> Content-Type: text/plain; charset=us-ascii
>> 
>> Hi all,
>> Does anyone know how to install qmmm code like mopac to gmx5.1?
>> 
>> Best,
>> Xianchi
>> 
>> 
>> 
> -- 
> 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-requ...@gromacs.org.
-- 
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Re: [gmx-users] QMMM install on GMX5.1 (Xianchi Dong)

[Clinton King]

Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html

You will also need to set the following variable at install time:

-DGMX_QMMM_MOPAC=ON

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University


>
>1. QMMM install on GMX5.1 (Xianchi Dong)
>
>
> Message: 1
> Date: Fri, 14 Oct 2016 17:14:36 -0400
> From: Xianchi Dong <dongxian...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] QMMM install on GMX5.1
> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi all,
> Does anyone know how to install qmmm code like mopac to gmx5.1?
>
> Best,
> Xianchi
>
>
>
-- 
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

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[gmx-users] QMMM install on GMX5.1

[Xianchi Dong]

Hi all,
Does anyone know how to install qmmm code like mopac to gmx5.1?

Best,
Xianchi
-- 
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

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