Methylated Histidine topology file

From: Sujata Sovani (sujatas_at_scripps.edu)
Date: Mon Aug 31 2009 - 12:38:03 CDT

Hi All,

I am new to NAMD. I have made a topology file for an unusual residue - methylated histidine. Now I want to know if it makes sense
I have modified the protonated HIS in the topology file to include the -CH3 group on the NE2. I have kept the charge as +1.00 on the whole residue so distributed the charge on HE2 among the new -CH3.
I have deleted the entry 'DONOR HE2 NE2'.
In the IC table, I have changed the dihedral for the entry CE1, CD2, *NE2 Cz to be -178.2 and the BL between NE2 and CZ to be 1.4213. I have also included three new entries in the IC table owing to the three methyl hydrogens.

Would someone advice if the new topology file makes sense? If it does, should this be included as a patch in the topology file?
I am attaching the file and pasting it here.

Thank you.

--------------------------------

RESI HSM 1.00 ! Protonated and methylated His
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
ATOM HA HB 0.09 ! | | / ||
GROUP ! HA-CA--CB--CG (+) || HZ2
ATOM CB CT2 -0.05 ! | | \\ || |
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2CZHZ1
ATOM HB2 HA 0.09 ! O=C | \ |
ATOM CD2 CPH1 0.19 ! | HD2 HE2 HZ3
ATOM HD2 HR1 0.13
ATOM CG CPH1 0.19
GROUP
ATOM NE2 NR3 -0.51
ATOM HE2 H 0.44
ATOM CZ CT3 0.17
ATOM HZ1 HA3 0.09
ATOM HZ2 HA3 0.09
ATOM HZ3 HA3 0.09
ATOM ND1 NR3 -0.51
ATOM HD1 H 0.44
ATOM CE1 CPH2 0.32
ATOM HE1 HR2 0.18
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CE1 ND1
BOND NE2 CD2 N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 ND1 HD1 NE2 CZ HZ1 HZ2 HZ3
BOND CD2 HD2 CE1 HE1
DOUBLE O C CD2 CG NE2 CE1
IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1
IMPR NE2 CD2 CE1 CZ NE2 CE1 CD2 CZ
IMPR N -C CA HN C CA +N O
IMPR CD2 NE2 CZ HZ1 CD2 NE2 CZ HZ2
IMPR CD2 NE2 CZ HZ3
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HD1 ND1
DONOR HE2 NE2
ACCEPTOR O C
IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041
IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225
IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464
IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284
IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521
IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533
IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832
IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168
IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116
IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132
IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718
IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549
IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262
IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727
IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799
IC CE1 CD2 *NE2 CZ 1.3256 108.8200 178.2000 125.5200 1.4213
IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018
IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867
IC CD2 NE2 CZ HZ1 1.4213 126.5000 179.8000 109.5000 1.0899
IC CD2 NE2 CZ HZ2 1.4213 126.5000 59.8000 109.5000 1.0899
IC CD2 NE2 CZ HZ3 1.4213 126.5000 60.8000 109.5000 1.0899


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