Yamin, Peyman wrote:
OH! And a (-1) Alanine I can never have since pdb2gmx has no option for that?
It's my C-Terminus in the end! :-|
If the C-terminus bears the charge, then simply choose COO- as your C-terminus.
If the sidechain is somehow deprotonated, then you have to come up with the
parameters for yourself.
-Justin
________________________________________ Von: [email protected]
[[email protected]] im Auftrag von Justin A. Lemkul
[[email protected]] Gesendet: Montag, 29. Juni 2009 16:53 An: Discussion list
for GROMACS users Betreff: Re: [gmx-users] protonation state with pdb2gmx
Yamin, Peyman wrote:
Hello,
with pdb2gmx I want to choose the protonation state of a GLN interactively.
When I choose +1 protonation state, I get the following error: Residue
'QLN' not found in residue topology database. But the program has itself
suggested the QLN as the name of this protonation state!!
Then you've chosen a force field for which the name QLN simply doesn't apply
:)
In fact, the only force field with QLN is OPLS.
-Justin
Would be pleased by your comments! cheers, Peyman
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-- ========================================
Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of
Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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