[gmx-users] Parametrisation of the heteroatomic pdb
jmsstarlight at gmail.com
Fri Oct 28 20:07:49 CEST 2011
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 ?
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.
>> You have to build capping groups onto the termini. See, for
>> instance the [ACE] and [NME] groups in the .rtp file.
> 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
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