[gmx-users] question
Andrew Bostick
andrew.bostick1 at gmail.com
Sat May 16 20:30:08 CEST 2015
Dear Justin
In pdb file, I corrected the distance between the two residues I want
bonded together to form the isopeptide bond (within 10% of my criterion
(0.13 nm). The new distance is 0.128 nm.
I used following specbond.dat, residuetyps.dat and aminoacids.rtp files.
---------------------------------------------------
specbond.dat:
9
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 1 HEM FE 2 0.25 CYS2 HEME
CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
MET SD 1 HEM FE 1 0.24 MET HEME
CO C 1 HEME FE 1 0.19 CO HEME
CYM SG 1 CYM SG 1 0.2 CYS2 CYS2
GLU CD 1 LYS NZ 1 0.13 GLU2 LYS2
---------------------------------------------------
residuetyps.dat (I added these two lines to the residuetyps.dat file):
GLU2 Protein
LYS2 Protein
---------------------------------------------------
aminoacids.rtp
[ LYS2 ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH2 0.00000 1
CG CH2 0.00000 2
CD CH2 0.00000 2
CE CH2 0.00000 2
NZ NT -0.28000 3
HZ1 H 0.28000 3
HZ2 H 0.00000 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
CB CG gb_26
CG CD gb_26
CD CE gb_26
CE NZ gb_20
NZ HZ1 gb_2
NZ HZ2 gb_2
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
CA CB CG ga_14
CB CG CD ga_14
CG CD CE ga_14
CD CE NZ ga_14
CE NZ HZ1 ga_10
CE NZ HZ2 ga_10
HZ1 NZ HZ2 ga_9
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
N CA CB CG gd_17
CA CB CG CD gd_17
CB CG CD CE gd_17
CG CD CE NZ gd_17
CD CE NZ HZ1 gd_14
---------------------------------------------------
[ GLU2 ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH2 0.00000 1
CG CH2 0.00000 1
CD C 0.380 2
OE1 OM -0.380 2
OE2 OM 0.00000 2
C C 0.380 3
O O -0.380 3
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
CB CG gb_26
CG CD gb_26
CD OE1 gb_5
CD OE2 gb_5
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
CA CB CG ga_14
CB CG CD ga_14
CG CD OE1 ga_21
CG CD OE2 ga_21
OE1 CD OE2 ga_37
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
CD OE1 OE2 CG gi_1
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
N CA CB CG gd_17
CA CB CG CD gd_17
CB CG CD OE2 gd_20
---------------------------------------------------
After using pdb2gmx, topology file was created without any error and
problem.
I checked these two residues (GLU380 and LYS540) in topology file, as
follows:
; residue 380 GLU rtp GLU q -1.0
1595 N 380 GLU N 705 -0.28 14.0067 ;
qtot -2.28
1596 H 380 GLU H 705 0.28 1.008 ;
qtot -2
1597 CH1 380 GLU CA 706 0 13.019 ;
qtot -2
1598 CH2 380 GLU CB 706 0 14.027 ;
qtot -2
1599 CH2 380 GLU CG 706 0 14.027 ;
qtot -2
1600 C 380 GLU CD 707 0.27 12.011 ;
qtot -1.73
1601 OM 380 GLU OE1 707 -0.635 15.9994 ;
qtot -2.365
1602 OM 380 GLU OE2 707 -0.635 15.9994 ;
qtot -3
1603 C 380 GLU C 708 0.38 12.011 ;
qtot -2.62
1604 O 380 GLU O 708 -0.38 15.9994 ;
qtot -3
; residue 540 LYS rtp LYSH q +1.0
1028 N 540 LYS N 465 -0.28 14.0067 ;
qtot -1.28
1029 H 540 LYS H 465 0.28 1.008 ;
qtot -1
1030 CH1 540 LYS CA 466 0 13.019 ;
qtot -1
1031 CH2 540 LYS CB 466 0 14.027 ;
qtot -1
1032 CH2 540 LYS CG 467 0 14.027 ;
qtot -1
1033 CH2 540 LYS CD 467 0 14.027 ;
qtot -1
1034 CH2 540 LYS CE 468 0.127 14.027 ;
qtot -0.873
1035 NL 540 LYS NZ 468 0.129 14.0067 ;
qtot -0.744
1036 H 540 LYS HZ1 468 0.248 1.008 ;
qtot -0.496
1037 H 540 LYS HZ2 468 0.248 1.008 ;
qtot -0.248
1038 H 540 LYS HZ3 468 0.248 1.008 ;
qtot 0
1039 C 540 LYS C 469 0.38 12.011 ;
qtot 0.38
1040 O 540 LYS O 469 -0.38 15.9994 ;
qtot 0
In both of them, my new entries (GLU2 and LYS2) have not used. Why?
Please check my charge and charge groups in these two new entries.
Is my manner wrong?
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