The last column in your rtp entry holds the chargegroup numbers. The
cgnr column in your top file looks just like it. Amber03 was not
parameterized with charge groups, so the atoms are not groupt together
as you can see.
Erik
leila karami skrev:
Dear Erik
thank for your answer.
my rtp file for amber 03 force field is as follow :
[ NGLY ]
[ atoms ]
N amber99_39 0.29430 1
H1 amber99_17 0.16420 2
H2 amber99_17 0.16420 3
H3 amber99_17 0.16420 4
CA amber99_11 -0.01000 5
HA1 amber99_28 0.08950 6
HA2 amber99_28 0.08950 7
C amber99_2 0.61630 8
O amber99_41 -0.57220 9
and my top file is as follow :
[ atoms
]
; nr type resnr residue atom cgnr charge mass
1 amber99_39 1 NGLY N 1 0.2943 14.01
2 amber99_17 1 NGLY H1 2 0.1642 1.008
3 amber99_17 1 NGLY H2 2 0.1642 1.008
4 amber99_17 1 NGLY H3 2 0.1642 1.008
5 amber99_11 1 NGLY CA 3 -0.01 12.01
6 amber99_28 1 NGLY HA1 4 0.0895 1.008
7 amber99_28 1 NGLY HA2 5 0.0895 1.008
8 amber99_2 1 NGLY C 6 0.6163 12.01
9 amber99_41 1 NGLY O 7 -0.5722 16
what relation is there between both of my rtp and top file in above ?
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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