[gmx-users] OPLS definition of Phenyl palmitate

[Justin Lemkul]

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> 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
>>
>>
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>

-- 
==================================================

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 | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================