[gmx-users] OPLS definition of Phenyl palmitate

[Ebert Maximilian]

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 <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> 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 <m.ebert at umontreal.ca<mailto:m.ebert at umontreal.ca>> 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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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