Dear all,
To follow up on my problem a bit and perhaps add a bug, I have looked at Tyrosine as an example and something puzzles me a bit.
In the "parm/parm10.dat" (I am using Amber11 just FYI). There are sections with parameters for Tyrosine as shown here below. Some are said not be in use anymore and some are said to replace these old parameters.
What puzzles me is that it seems that the CZ (atomname) has been changed in atomtype from C to CA.
However, when I look in "lib/amino10.lib" and "prep/amino10.in" the atomtype is still C and not CA.
Is this a bug/error or is this changed somewhere else?
Is this the same for ff12 in Amber12?
Best regards,
Jesper
C -CA 469.0 1.409 JCC,7,(1986),230; (not used any more in TYR)
C -OH 450.0 1.364 JCC,7,(1986),230; (not used any more for TYR)
CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR
CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR
CA-OH 450.0 1.364 substituted for C-OH in tyr
CA-C -OH 70.0 120.00 AA (not used in tyr)
CA-C -OS 70.0 120.00 phosphotyrosine
C -CA-HA 50.0 120.00 AA (not used in tyr)
CA-CA-OH 70.0 120.00 replacement in tyr
CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes
CT-CT-CA 63.0 114.00 AA phe tyr (SCH JPC 79,2379)
CX-CT-CA 63.0 114.00 AA phe tyr (SCH JPC 79,2379) (was CT-CT-CA)
C -OH-HO 50.0 113.00 (not used in tyr anymore)
CA-OH-HO 50.0 113.00 replacement in tyr
CA-CA-C -OH 1.1 180. 2. (not used in tyr!)
CA-CA-CA-OH 1.1 180. 2. in tyr
On Sep 14, 2012, at 4:37 PM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
> Hi all,
>
> I am trying to parameterize a ligand that contains a deprotonated phenol group.
> The oxygen is not exactly double bonded, but the C-O bond distance is very short (1.24 based on QM optimizations). Using parmcal this distance places it between a double bond (1.23) and a conjugated bond (1.26).
>
> I have been looking through the force field files for amber and gaff for a good atomtype for the oxygen, but I am not sure which one to use.
> Does anyone have a good suggestion for one to use, or should I proceed to create one on my own?
> In either case, would you suggest adding special bonded parameters for this bond, perhaps using values from parmcal?
>
> Best regards,
> Jesper
>
>
>
> ---
> Jesper Sørensen, Ph.D.
> Postdoctoral Researcher, Amarolab
> Department of Chemistry and Biochemistry
> University of California, San Diego
> 9500 Gilman Drive
> La Jolla, CA 92093-0340
> http://amarolab.ucsd.edu
>
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Received on Mon Sep 17 2012 - 10:00:03 PDT
