[gmx-users] methylated HSP

[Justin Lemkul]

On 7/4/17 1:32 PM, Emma Ahlstrand wrote:
> Hi,
> 
> I am going to simulate a protein with a methylated histidine in Gromacs using CHARMM36 FF. I name the modified aminoacid HIC, the structure is attached in pdf file.
> 
> I have followed the discussion in https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=15364&page=all
> but I cannot see that NR3 is the proper atomtype. I have tried to add bonds, angles and dihedrals for NR3 and the methyl,:
> 
> [ bondtypes ]
> ;      i        j  func           b0           kb
>       NR3      CT3     1   0.149         167360.00 ; inserted for methylated HIS (HIC)
> [ angletypes ]
> ;      i        j        k  func       theta0       ktheta          ub0          kub
>       NR3      CT3      HA3     5   107.500000   472.792000   0.00000000         0.00 ;inserted for HIC
> [ dihedraltypes ]
> ;      i        j        k        l  func         phi0         kphi  mult
>       NR3     CPH2      NR3      CT3     9   180.000000    12.552000     2 ; inserted for HIC
>       HR2     CPH2      NR3      CT3     9   180.00        12.552000     2 ; inserted for HIC
>       HR1     CPH1      NR3      CT3     9     0.000        8.368000     2 ; inserted for HIC
>      CPH1     CPH1      NR3      CT3     9   180.00        50.208000     2 ; inserted for HIC
>       CT1      CT2     CPH1      NR3     9     0.00000      0.000000     1 ; inserted for HIC
>      CPH1      NR3      CT3      HA3     9     0.00000      0.000000     1 ; inserted for HIC
>      CPH2      NR3      CT3      HA3     9     0.000000     0.000000     1 ; inserted for HIC
> [ dihedraltypes ]
> ; 'improper' dihedrals
> ;      i        j        k        l  func         phi0         kphi
>       NR3     CPH1     CPH2      CT3     2     0.0000      10.041600 ; inserted for HIC
>       NR3     CPH2     CPH1      CT3     2     0.00000     10.041600 ; inserted for HIC
>       CT2     CPH1      NR3     CPH1     2     0.00000      0.00000  ; inserted for HIC
>       CT2      NR3     CPH1     CPH1     2     0.00000      0.00000  ; inserted for HIC
>      CPH1     CPH1      NR3      HR1     2     0.00000      0.00000 ; inserted for HIC
>      CPH1      NR3     CPH1      HR1     2     0.00000      0.00000 ; inserted for HIC
>      CPH2      NR3      NR3      HR2     2     0.00000      0.00000 ; inserted for HIC
> 
> but ended up with "No default U-B types" for CPH1 NR3 CT3 and CPH2 NR3 CT3
> Anyone who is interested to help me find the problem?
> 
> Or is there a better atomtype for the nitrogen in the HIS/imidazole ring where a methyl group can be attached. I tried NG321, but then I ran into troubles when attaching to CPH1 and CPH2.
> 

Don't mix CGenFF types with normal CHARMM types.

All you need to do is find an analogous angle to CPH1(2)-NR3-CT3.  There are 
methylated nucleobases in CHARMM that you can look at, which the thread you 
quote mentions.

-Justin

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

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

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