Dear Adam,
Concerning the protonated histidine resdiue this looks like a big
cuisine... You might be interested in computing your own set of charge
values using R.E.D. Server; charges for ff03 are derived by choosing
the RESP-A1B charge model.
See
http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
If you read the tutorial at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
see the two following sections:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
vs
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
as you can see the N-term, C-term and central fragments of a new
residue can be directly obtained from the corresponding dipeptide.
---
Concerning Norleucine
http://en.wikipedia.org/wiki/Norleucine you can
obviously apply the same strategy in R.E.D. Server i.e.:
- create the dipeptide of norleucine in the PDB file format; here
think to what conformation(s) you want to involve in charge derivation
- run R.E.D. Server/Ante_R.E.D. 2.0 to generate the P2N file for the
different conformations of Norleucine you are interested in.
- merge with a text editor these P2N files to create a single P2N file
for the the different conformations of the norleucine dipeptide (a
single P2N file per molecule)
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#EXAMPLE-P2N-FILE
- run R.E.D. Server/R.E.D. IV
atom typing is not carried out by R.E.D. IV (perl) - our new code
R.E.D. Python does perform atom typing (and far more) - you could send
a request from the private assistance service (see
http://q4md-forcefieldtools.org/REDS/faq.php#5) to ask for
post-processing of the data generated by R.E.D. Perl by using R.E.D.
Python.
regards, Francois
> While double checking to make sure I had set my system up properly, I was
> looking through the charges and realized that the charge on protonated
> histidine inside of Amberff03 did not add up to +1 (they add up to about
> +0.45). I cross referenced the DESMOND implementation of the Amber03 force
> field and noticed that they had flipped a few signs around. In particular,
> the CA, HA, and ND1 have their signs flipped in DESMOND. The charges in
> the DESMOND implementation correctly sum up to 1.
>
> I saw this mentioned earlier in the mailing list (
> http://archive.ambermd.org/200803/0171.html) and I noticed that Dr.
> Walker's charges match those in the DESMOND implementation, whereas the
> original poster's charges match those in my own Amber force field file;
> this discrepancy is not addressed in that former email. I am using
> Amber12/AmberTools13. The tools were just updated yesterday. Any thoughts?
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Received on Wed Sep 25 2013 - 02:00:02 PDT
