[gmx-users] 3. gromacs with turbomole? (Francesca L?nstad Bleken)

[Groenhof, Gerrit]

Hi,

Did you try if it works?

If not, you can adapt the general gau gaussian script to molpro input (http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian). 

I assume that is also the how the turbomole interface has been done.

Gerrit




Hi,

I am looking for viable systems for doing QM/MM calculations and as I have experience with both Turbomole and GROMACS I am wondering if
there is anyone using these two together. I have found this ("The Quick and Dirty GROMACS-TURBOMOLE interface") at https://github.com/rmera/qdgt ,
but it is 6 years old and I am not sure whether it is applicable with newer versions of both programs. Anyone working on this or have any tips?

Best regards,
Francesca


------------------------------

Message: 4
Date: Wed, 2 May 2018 09:07:38 -0400
From: MD <refmac5 at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] index two groups for the distance calculation
Message-ID:
        <CAPPXTgQb43qHHpsCP4hOAk3FkRuuA1QfC9kGX05Rit3Z-FY5FQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi Gromacs,

I was trying to index two amino acids to two groups and calculate the
distance between them.

I used the command

"gmx make_ndx -f md.gro -o index.ndx"

and tried to select residue 159 from chain A (group of r_159) and residue
15 from chain B. However, when I used the  "l" function to list all the
residues I was not able to find the residue 15 from chain B. I was able to
find it based on the sequence but it has a different number 372, instead of
15 in its original structure of chain B. I think gromacs renumbered the
whole sequence and combined chain A and B? When I select r 372, i was told
it is an empty group.

Can someone help me here, please?

Thanks in advance,

Ming


------------------------------

Message: 5
Date: Wed, 02 May 2018 13:17:50 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] index two groups for the distance calculation
Message-ID:
        <CAMNuMASiRTwJgkZLR-0u5jz12QSkf5rhU4WhiBQXZ6aThc7FnQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

Look at the contents of the .gro file with the "less" tool and see what the
numbering is :-)

Mark

On Wed, May 2, 2018 at 3:07 PM MD <refmac5 at gmail.com> wrote:

> Hi Gromacs,
>
> I was trying to index two amino acids to two groups and calculate the
> distance between them.
>
> I used the command
>
> "gmx make_ndx -f md.gro -o index.ndx"
>
> and tried to select residue 159 from chain A (group of r_159) and residue
> 15 from chain B. However, when I used the  "l" function to list all the
> residues I was not able to find the residue 15 from chain B. I was able to
> find it based on the sequence but it has a different number 372, instead of
> 15 in its original structure of chain B. I think gromacs renumbered the
> whole sequence and combined chain A and B? When I select r 372, i was told
> it is an empty group.
>
> Can someone help me here, please?
>
> Thanks in advance,
>
> Ming
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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------------------------------

Message: 6
Date: Wed, 2 May 2018 11:42:58 -0400
From: MD <refmac5 at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] index two groups for the distance calculation
Message-ID:
        <CAPPXTgSpzSiS4vy+TAjXNpNHRgdSrQbF=heGHjqC+ROrvvdDsw at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi Mark,
They have the correct number in the .gro file. Chain A has residues from 6
to 330 which contains my residue 159, chain B has residues from 1 to 30
which contains my residue 15. So if I select "r 15" when indexing there
will be two residue 15 selected, one from chain A and one from chain B. Is
there a way to specifically select residue 15 from chain B?
Thank you,
Ming

On Wed, May 2, 2018 at 9:17 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Look at the contents of the .gro file with the "less" tool and see what the
> numbering is :-)
>
> Mark
>
> On Wed, May 2, 2018 at 3:07 PM MD <refmac5 at gmail.com> wrote:
>
> > Hi Gromacs,
> >
> > I was trying to index two amino acids to two groups and calculate the
> > distance between them.
> >
> > I used the command
> >
> > "gmx make_ndx -f md.gro -o index.ndx"
> >
> > and tried to select residue 159 from chain A (group of r_159) and residue
> > 15 from chain B. However, when I used the  "l" function to list all the
> > residues I was not able to find the residue 15 from chain B. I was able
> to
> > find it based on the sequence but it has a different number 372, instead
> of
> > 15 in its original structure of chain B. I think gromacs renumbered the
> > whole sequence and combined chain A and B? When I select r 372, i was
> told
> > it is an empty group.
> >
> > Can someone help me here, please?
> >
> > Thanks in advance,
> >
> > Ming
> > --
> > 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!
>
> * 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.
>


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