James Starlight wrote:
Justin?
So As I understood the aminoacids.rtp of current force field must
include topology for such caps.
Yes. Any residue whatsoever that you wish to process with pdb2gmx must be
present in an .rtp file.
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 ?
Do not mix and match force fields. Even if you can hack it into working, the
results will be absolute garbage. If you need a topology for a specific force
field, refer to the parameterization link I posted before. Deriving parameters
for new residues in an existing force field is a task that may take weeks or
months to do properly and hence is considered an expert topic. I have nothing
more to contribute on that issue. The archives are filled with tips and
discussions on how to go about such things.
-Justin
James
2011/10/28 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
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
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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========================================
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
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