[gmx-users] Atom definition in atomname2type.n2t file

[Adnan Shahriar]

Thank you very much Dr. Warren.

Adnan

On Sun, Oct 22, 2017 at 3:22 PM, Dallas Warren <dallas.warren at monash.edu>
wrote:

> Since the .n2t file has a set format, easiest way is to write yourself
> a script that will generate the required combinations and print out
> the result for you.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 21 October 2017 at 04:55, Adnan Shahriar
> <undefined.shahriar at gmail.com> wrote:
> > Hi,
> >
> > I like to use x2top command to generate a primitive topology file for
> > Graphene Oxide, where I have defined new Atoms with new Types. This
> > requires a file, *atomname2type.n2t *that contains data like this,
> >
> > C    opls_157    -0.18 12.011 4    H 0.108   H 0.108   H 0.108   C 0.150
> > C    opls_158    -0.12  12.011 4    H 0.108   H 0.108   C 0.150   C 0.150
> > C    opls_157    0.145  12.011 4    H 0.108   O 0.141   H 0.108   C 0.150
> > C    opls_157    0.145  12.011 4    H 0.108   H 0.108   O 0.108   C 0.150
> > ....
> >
> > I have modified it like this,
> >
> > CAg   CAg    0.00      12.011  3    CAg 0.141   CAg 0.141   CAg 0.141
> > CTal   CTal    0.00      12.011  3    CAg 0.141   CAg 0.141   CAg 0.141
> > CTal   CTal    0.00      12.011  3    CAg 0.141   CToh 0.141   CAg 0.141
> > CTal   CTal    0.00      12.011  3    CAg 0.141   CAe 0.141   CAg 0.141
> > CTal   CTal    0.00      12.011  3    CAg 0.141   CToh 0.141   CAe 0.141
> > CTal   CTal    0.00      12.011  3    CTal 0.141   CAg 0.141   CAg 0.141
> > .......
> >
> > But this is too tiring as it requires a lot combination. So what I want
> to
> > do is assign CAg, CTal as C and make it very simple like this,
> >
> > CAg   CAg    0.00      12.011  3    C 0.141   C 0.141   C 0.141
> > CTal   CTal    0.00      12.011  3    C 0.141   C 0.141   C 0.141
> > ....
> >
> > So, how can I do that?
> >
> > Thanks in advance.
> >
> > Adnan
> > undefined.shahriar at gmail.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!
>
> * 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.
>