Re: [AMBER] phenylalanine amide

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Thu, 02 Sep 2010 20:43:07 +0200

Dear Francesco,

Sorry, I was not in the lab & did not have any ssh connection...

> I am looking for Amber-type charges and radii for a modified residue:
> phenylalanine amide (amidated phenylalanine). I have no suitable ab
> initio software for using RED. Thanks for providing data or literature
> reference.

You know "Firefly" is fast, provided at no cost, works on
Mac/Windows/UNIX, does not need to be compiled and is fully interfaced
by R.E.D.

Anyway, you can find your NH2 fragment .
http://q4md-forcefieldtools.org/Help/Francesco/
http://q4md-forcefieldtools.org/Help/Francesco.tgz

I used three models as test cases:
- Cornell et al. FF:
http://q4md-forcefieldtools.org/Help/Francesco/R.E.D./RED-vIII.4.log
- Weiner et al. FF (the one you need if I well understood):
http://q4md-forcefieldtools.org/Help/Francesco/R.E.D.-2/RED-vIII.4.log

                                 WARNING:
                 "ESP-A2" & "ESP-C2" charge models are outdated
        Nowdays, they should _not_ be used in atomic charge derivation
    These models are only available in R.E.D. for compatibility with the past

                                 WARNING:
    "ESP-A2" & "ESP-C2" charge models & multi-molecule ESP charge derivation
                         are not supported in R.E.D.-III.x
     Job(s) will be performed as a batch; each molecule being independent

[fyd.lynx R.E.D.-2/Data-RED]$ grep "ESP rel" */*/out*
Mol_m1/output1_m1: ESP relative RMS (SQRT(chipot/ssvpot)) 0.12678
Mol_m1/output1_m1.sm: ESP relative RMS (SQRT(chipot/ssvpot)) 0.31761
Mol_m2/output1_m2: ESP relative RMS (SQRT(chipot/ssvpot)) 0.07340
Mol_m2/output1_m2.sm: ESP relative RMS (SQRT(chipot/ssvpot)) 0.31851
Mol_m3/output1_m3: ESP relative RMS (SQRT(chipot/ssvpot)) 0.08973
Mol_m3/output1_m3.sm: ESP relative RMS (SQRT(chipot/ssvpot)) 0.32505

I would vote for using Mol_m1/Mol_m1-o1-sm.mol2; see
http://q4md-forcefieldtools.org/Help/Francesco/R.E.D.-2/Data-RED/Mol_m1/punch1_m1.sm
&
http://q4md-forcefieldtools.org/Help/Francesco/R.E.D.-2/Data-RED/Mol_m1/punch2_m1.sm (charge equivalencing is carried a posteriori to the fit for the Weiner et al. force
field)

The FF library:
http://q4md-forcefieldtools.org/Help/Francesco/R.E.D.-2/Data-RED/Mol_m1/Mol_m1-o1-sm.mol2

You just need to define a head for the nitrogen atom in
Mol_m1-o1-sm.mol2, to combine PHE & NH2

regards, Francois



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Received on Thu Sep 02 2010 - 12:00:02 PDT