[gmx-users] methylated HSP

[Emma Ahlstrand]

pdf attached now.

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Emma Ahlstrand
PhD student

Linnaeus University
Faculty of Health and Life Sciences
391 82 Kalmar / 351 95 Växjö
Sweden

+46 772 28 80 00 Telephone exchange
+46 480 44 61 52 Direct
+46 739 05 71 86 Mobile
emma.ahlstrand at lnu.se
http://lnu.se/ccbg
Lnu.se

Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden.
________________________________________
From: Emma Ahlstrand
Sent: Tuesday, July 04, 2017 7:32 PM
To: gmx-users at gromacs.org
Subject: methylated HSP

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.

Best regards,
Emma

-----------------------------------------------------------
Emma Ahlstrand
PhD student

Linnaeus University
Faculty of Health and Life Sciences
391 82 Kalmar / 351 95 Växjö
Sweden

+46 772 28 80 00 Telephone exchange
+46 480 44 61 52 Direct
+46 739 05 71 86 Mobile
emma.ahlstrand at lnu.se
http://lnu.se/ccbg
Lnu.se

Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden.