[gmx-users] Parametrisation of the heteroatomic pdb

[James Starlight]

Justin?

So As I understood the aminoacids.rtp of current force field must include
topology for such caps.

But for example If I have only topology on such groups for another ff could
I include it to the amber FF? If no where I could find such topology ?


James

2011/10/28 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>>
>> I understood that but how I can add that groups to termi of the bowh of my
>> chains ?
>>
>> I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS.
>> May be Amber ff didnt support this feature ?
>>
>>
> pdb2gmx does not build things that aren't there.  Your input coordinate
> file needs to have the capping groups present, with all atoms named as the
> .rtp entries expect them, hence the suggestion to investigate the [ACE] and
> [NME] directives.
>
> -Justin
>
>
>
>> James
>>
>>
>>    You have to build capping groups onto the termini.  See, for
>>    instance the [ACE] and [NME] groups in the .rtp file.
>>
>>    -Justin
>>
>>
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111028/9e0d80be/attachment.html>