[gmx-users] X2top usage

[Ben Tam]

Dear David,


Thank you for your suggestion. At the end I just gave up and write a code to solve the problem. Is there a better way/software to get the connectivity map of a crystallise structure?


Best regards,


Benjamin Tam


________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: 07 September 2016 14:33
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] X2top usage

On 07/09/16 13:48, Ben Tam wrote:
> Dear gromacs user.
>
>
> I am using gmx x2top to write a rough connectivity map for the crystal structure that I am using. In the conf.gro file, there are many ions with no bond to any other molecules. How do I specify that on .n2t file? Because when I do specify it with:
>
> Mg   Mg          0.000  24.3050 0

The software is way past it's best before date.
How about leaving out the Mg and putting them in manually later?
>
>
> It is still giving me the error of :
>
>
> Can not find forcefield for atom Mg-1245 with 0 bonds
> Can not find forcefield for atom Mg-1254 with 0 bonds
> Can not find forcefield for atom Mg-1263 with 0 bonds
> Can not find forcefield for atom Mg-1272 with 0 bonds
> Can not find forcefield for atom Mg-1281 with 0 bonds
> Can not find forcefield for atom Mg-1290 with 0 bonds
> Can not find forcefield for atom Mg-1299 with 0 bonds
> Can not find forcefield for atom Mg-1308 with 0 bonds
> Can not find forcefield for atom Mg-1317 with 0 bonds
> Can not find forcefield for atom Mg-1326 with 0 bonds
> Can not find forcefield for atom Mg-1335 with 0 bonds
> Can not find forcefield for atom Mg-1344 with 0 bonds
> Can not find forcefield for atom Mg-1353 with 0 bonds
> Can not find forcefield for atom Mg-1362 with 0 bonds
> Can not find forcefield for atom Mg-1371 with 0 bonds
> Can not find forcefield for atom Mg-1380 with 0 bonds
> Can not find forcefield for atom Mg-1389 with 0 bonds
> Can not find forcefield for atom Mg-1398 with 0 bonds
> Can not find forcefield for atom Mg-1407 with 0 bonds
> Can not find forcefield for atom Mg-1416 with 0 bonds
> Can not find forcefield for atom Mg-1425 with 0 bonds
> Can not find forcefield for atom Mg-1434 with 0 bonds
> Can not find forcefield for atom Mg-1435 with 0 bonds
>
> Thank you very much,
>
> Best regards,
>
> Ben
>
>
>


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
Folding.bmc.uu.se - David van der Spoel<http://folding.bmc.uu.se/>
folding.bmc.uu.se
Saturday, 08 February 2014 Time flies! Under 2013 Moreno Marcellini came over from the chemistry department as a postdoc, but by the time I write this his contract ...



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