On 6/14/17 12:25 AM, Rana Rehan Khalid wrote:
Hi
I have read the chapter 5 of manual but i am confuse how can i add residue
into heme atom of .rtp ff
this is the coordinate due to which error come
HETATM 1529 O01 HEM 187 3.996 19.101 70.594 0.00
0.00 O
kindly guide me how i can make changes in the rtp file and .atp so that
this error remove
here is the heme rtp part of my selected ff where i can add O01 and also
tell me these 4 column and these values and tell me which value i add for
O01 like (FE FE 0.40000 0 )
You should refer back to the manual if the contents of these files are not
clear. You're seeking to introduce new parameters for an oxygen-bound form of
heme; this may require very complex parametrization work. Modifying an .rtp
file is trivial; it's just text. Putting realistic parameters into it is a
whole other matter. Check the literature for any existing efforts to avoid
duplicated work.
-Justin
[ HEME ]
[ atoms ]
FE FE 0.40000 0
NA NR -0.10000 0
NB NR -0.10000 0
NC NR -0.10000 0
ND NR -0.10000 0
CHA C -0.10000 1
HHA HC 0.10000 1
C1A C 0.00000 2
C2A C 0.00000 2
C3A C 0.00000 2
C4A C 0.00000 2
CMA CH3 0.00000 3
CAA CH2 0.00000 4
CBA CH2 0.00000 4
CGA C 0.27000 5
O1A OM -0.63500 5
O2A OM -0.63500 5
CHB C -0.10000 6
HHB HC 0.10000 6
C1B C 0.00000 7
C2B C 0.00000 7
C3B C 0.00000 7
C4B C 0.00000 7
CMB CH3 0.00000 8
CAB CR1 0.00000 9
CBB CH2 0.00000 9
CHC C -0.10000 10
HHC HC 0.10000 10
C1C C 0.00000 11
C2C C 0.00000 11
C3C C 0.00000 11
C4C C 0.00000 11
CMC CH3 0.00000 12
CAC CR1 0.00000 13
CBC CH2 0.00000 13
CHD C -0.10000 14
HHD HC 0.10000 14
C1D C 0.00000 15
C2D C 0.00000 15
C3D C 0.00000 15
C4D C 0.00000 15
CMD CH3 0.00000 16
CAD CH2 0.00000 17
CBD CH2 0.00000 17
CGD C 0.27000 18
O1D OM -0.63500 18
O2D OM -0.63500 18
thanks
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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