Maybe this is of interest to others so I will write what I did. I built a
phenyl acetate and methyl acetate:
O_2
||
CA - CA C_2
/ \ / \
CA CA - OS CT
\ /
CA - CA
O_2
||
C_2
/ \
CT - OS CT
And I did a conformation search of the two molecules using QM/MM. After finding
the best ideal gas solution I looked at the dihedral energy profile of CT OS
C_2 O_2, CT OS C_2 CT, CA OS C_2 O_2 and CA OS C_2 CT. The pairs basically
matched with the same energy minimum at the same angle. So I presume now that
with a small error the approximation can be used. Of course I am not an expert
as you can tell so if you have any additional thoughts please let me know.
Max
On Jun 8, 2015, at 9:35 AM, Ebert Maximilian
<[email protected]<mailto:[email protected]>> wrote:
Thanks for your response. First of all I must say it is a bit strange that OPLS
has the atom types of phenyl ester but not the corresponding dihedral angels to
support it. But I see your point but could you elaborate on how I could
evaluate this? How can I calculate those profiles?
Thanks,
Max
On Jun 7, 2015, at 9:49 AM, Justin Lemkul
<[email protected]<mailto:[email protected]><mailto:[email protected]>> wrote:
On 6/5/15 6:08 PM, Ebert Maximilian wrote:
Hi,
a small little update. I saw that CT OS C_2 O_2 and CT OS C_2 CT are defined
OPLS/AA. I used these parameters now to define CA OS C_2 O_2 and CA OS C_2 CT
in OPLS/AA. Any thoughts on that? I really have difficulties to visualize
dihedral angles and I am not sure if this would actually give roughly the same
geometry or not.
The determining factor is whether or not the QM and MM energy profiles match as
those dihedrals are rotated.
-Justin
Thanks and have a good weekend.
Max
On Jun 5, 2015, at 4:38 PM, Ebert Maximilian
<[email protected]<mailto:[email protected]><mailto:[email protected]>>
wrote:
Dear list,
I ran into some problem to define the topology of phenyl palmitate. My main
problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of
the molecule without hydrogen (I hope it turns out to be readable in the email):
O17
||
C21 - C20 C16 (C)n
/ \ / \ / \
C22 C19 - O18 C15 C1
\ /
C23 - C24
I think I defined the atom types correctly:
[ atoms ]
; nr type resi res atom cgnr charge mass
1 opls_768 1 PNR C22 4 -0.1952 12.01100
2 opls_145 1 PNR C21 5 -0.0500 12.01100
3 opls_145 1 PNR C20 6 -0.1550 12.01100
4 opls_145 1 PNR C23 7 -0.0500 12.01100
5 opls_145 1 PNR C24 8 -0.1550 12.01100
6 opls_472 1 PNR C19 9 0.1591 12.01100
7 opls_473 1 PNR O18 10 -0.3732 15.99940
8 opls_465 1 PNR C16 11 0.6491 12.01100
9 opls_466 1 PNR O17 12 -0.5100 15.99940
10 opls_136 1 PNR C15 13 -0.1264 12.01100
11 opls_136 1 PNR C14 14 -0.0804 12.01100
12 ….
The problem is now in the ester since there is no dihedral definition of CA OS
C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is
Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I
understand 472 correctly? How can I resolve the missing two dihedral angles?
I also wanted to know if somebody has an idea what is meant by: AA C: esters
- for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case
to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since
they are the R of the ester?
Thank you very much for your advice,
Max
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
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Baltimore, MD 21201
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