Sorry to paste big files here. (.pdb file and processed.top )
pdb file.
TITLE Protein
REMARK THIS IS A SIMULATION BOX
CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00
ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00
ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00
ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00
ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00
ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00
ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00
ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00
ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00
ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00
ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00
ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00
ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00
ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00
ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00
ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00
ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00
ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00
ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00
ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00
ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00
ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00
ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00
ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00
ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00
ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00
ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00
ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00
ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00
ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00
ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00
ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00
ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00
ATOM 34 N3 EMI 3 25.074 30.288 7.940 1.00 0.00
ATOM 35 C4 EMI 3 26.335 30.336 7.464 1.00 0.00
ATOM 36 N5 EMI 3 26.369 29.867 6.216 1.00 0.00
ATOM 37 C6 EMI 3 27.586 29.761 5.460 1.00 0.00
ATOM 38 C7 EMI 3 27.397 29.088 4.106 1.00 0.00
ATOM 39 C8 EMI 3 24.601 30.404 9.351 1.00 0.00
ATOM 40 H9 EMI 3 24.815 29.446 4.790 1.00 0.00
ATOM 41 H10 EMI 3 23.203 29.817 6.920 1.00 0.00
ATOM 42 H11 EMI 3 27.238 30.558 8.074 1.00 0.00
ATOM 43 H12 EMI 3 24.321 29.435 9.759 1.00 0.00
ATOM 44 H13 EMI 3 25.411 30.876 9.880 1.00 0.00
ATOM 45 H14 EMI 3 23.735 31.092 9.515 1.00 0.00
ATOM 46 H15 EMI 3 28.216 29.130 6.169 1.00 0.00
ATOM 47 H16 EMI 3 28.027 30.763 5.434 1.00 0.00
ATOM 48 H17 EMI 3 26.886 29.695 3.344 1.00 0.00
ATOM 49 H18 EMI 3 28.366 28.886 3.715 1.00 0.00
ATOM 50 H19 EMI 3 26.842 28.200 3.880 1.00 0.00
ATOM 51 S20 ETS 4 26.876 17.203 7.791 1.00 0.00
ATOM 52 O21 ETS 4 28.030 16.750 7.061 1.00 0.00
ATOM 53 O22 ETS 4 25.656 16.428 7.528 1.00 0.00
ATOM 54 O23 ETS 4 27.112 17.470 9.202 1.00 0.00
ATOM 55 O24 ETS 4 26.578 18.733 7.129 1.00 0.00
ATOM 56 C25 ETS 4 26.215 18.995 5.843 1.00 0.00
ATOM 57 C26 ETS 4 27.436 19.133 4.921 1.00 0.00
ATOM 58 H27 ETS 4 25.607 18.170 5.486 1.00 0.00
ATOM 59 H28 ETS 4 25.530 19.872 5.774 1.00 0.00
ATOM 60 H29 ETS 4 28.107 19.910 5.179 1.00 0.00
ATOM 61 H30 ETS 4 27.944 18.247 4.832 1.00 0.00
ATOM 62 H31 ETS 4 27.138 19.330 3.927 1.00 0.00
TER
ENDMDL
processed.top
;
; File 'p2.top' was generated
; By user: ndhumal (36026)
; On host: c63
; At date: Sun Sep 22 21:03:07 2013
;
; This is your topology file
; Protein
;
; Include forcefield parameters
; This force field uses a format that requires Gromacs 3.1.4 or later.
;
; References for the OPLS-AA force field:
;
; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
; J. Am. Chem. Soc. 118, 11225-11236 (1996).
; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998).
; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001).
; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J.
Phys. Chem. B 105, 6474 (2001).
;
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
; Derived from parsing of runfiles/alat.top.orig
;[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_135 CT 6 12.01100 -0.180 A 3.50000e-01 2.76144e-01
opls_136 CT 6 12.01100 -0.120 A 3.50000e-01 2.76144e-01
opls_140 HC 1 1.00800 0.060 A 2.50000e-01 1.25520e-01
opls_154 OH 8 15.99940 -0.683 A 3.12000e-01
7.11280e-01
opls_155 HO 1 1.00800 0.418 A 0.00000e+00
0.00000e+00
opls_159 CT 6 12.01100 0.265 A 3.50000e-01
2.76144e-01
opls_169 OH 8 15.99940 -0.700 A 3.07000e-01 7.11280e-01
opls_180 OS 7 15.99940 -0.400 A 2.90000e-01 5.85760e-01
opls_401 CL 17 35.45300 -1.000 A 4.40104e-01 4.18400e-01
opls_557 NA 7 14.00670 -0.257 A 3.25000e-01
7.11280e-01
opls_558 CR 6 12.01100 0.275 A 3.55000e-01
2.92880e-01
opls_561 CW 6 12.01100 -0.286 A 3.55000e-01
2.92880e-01
opls_563 HA 1 1.00800 0.078 A 2.42000e-01
1.25520e-01
opls_564 HA 1 1.00800 0.075 A 2.42000e-01
1.25520e-01
opls_273 CT 6 12.01100 -0.280 A 3.50000e-01 2.76144e-01
opls_271 C_3 6 12.01100 0.700 A 3.75000e-01 4.39320e-01
opls_272 O2 8 15.99940 -0.800 A 2.96000e-01 8.78640e-01
opls_440 P 15 30.97376 1.620 A 3.74000e-01 8.36800e-01
opls_441 O2 8 15.99940 -0.920 A 3.15000e-01 8.36800e-01
opls_442 OS 8 15.99940 -0.600 A 2.90000e-01 5.85760e-01
opls_443 CT 6 12.01100 0.300 A 3.50000e-01 2.76144e-01
opls_444 HC 1 1.00800 -0.030 A 2.50000e-01 1.25520e-01
opls_966 B 9 10.8110 1.1504 A 3.58140e-01 3.97500e-01
opls_967 F 9 18.99840 -0.5376 A 3.11810e-01 2.55200e-01
opls_968 CG 6 12.01100 -0.180 A 3.50000e-01 2.76144e-01
[ bondtypes ]
; i j func b0 kb
CR NA 1 0.13150 399200.0 ; HIS
CW NA 1 0.13780 357400.0 ; TRP,HIS
CW CW 1 0.13410 435200.0 ;
CT NA 1 0.14660 282000.0 ; copy from above for CytH+ (jtr
5-14-91)
CT CT 1 0.15290 224200.0 ; CHARMM 22 parameter file
CW HA 1 0.10800 307105.6 ; pyrrole- wlj
CR HA 1 0.10800 307105.6 ;
CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file
C_3 CT 1 0.15220 265265.6 ;
C_3 O2 1 0.12500 548940.8 ; GLU,ASP
O2 P 1 0.14800 439320.0 ; SUG(OL)
OS P 1 0.16100 192464.0 ; SUG(OL)
CT OS 1 0.14100 267776.0 ;
B F 1 0.13900 242680.0 ; J. Phys. Chem. B (2004), 108,
12978
; for glucose
CG CG 1 0.15290 224262.4 ; CHARMM 22 parameter file
CG HC 1 0.10900 284512.0 ; CHARMM 22 parameter file
CG OH 1 0.14100 267776.0 ;
HO OH 1 0.09450 462750.4 ; SUG(OL) wlj mod 0.96-> 0.945
CG OS 1 0.14100 267776.0 ;
[ angletypes ]
; i j k func th0 cth
CW NA CR 1 108.000 585.200 ; wlj -idem-
CW NA CT 1 125.600 585.200 ;
CR NA CT 1 126.400 585.200 ;
NA CR HA 1 125.100 292.600 ;
NA CR NA 1 109.800 585.200 ; HISP(OL)
NA CW CW 1 107.100 585.200 ;
NA CW HA 1 122.000 292.600 ; wlj
CW CW HA 1 130.900 292.600 ;
CT CT HC 1 110.700 313.200 ; CHARMM 22 parameter file
NA CT HC 1 110.700 313.200 ; CHARMM 22 parameter file
CT CT CT 1 112.700 836.800 ;
NA CT CT 1 112.700 836.800 ;
HC CT HC 1 107.800 276.200 ; CHARMM 22 parameter file
C_3 CT HC 1 109.500 292.880 ;
CT C_3 O2 1 117.000 585.760 ; GLU(OL) SCH JPC
79,2379
O2 C_3 O2 1 126.000 669.440 ; GLU(OL) SCH JPC
79,2379
O2 P O2 1 119.900 1171.520 ; SUG(OL)
O2 P OS 1 108.230 836.800 ; SUG(OL)
OS P OS 1 102.600 376.560 ; SUG(OL)
CT OS P 1 120.500 836.800 ;
HC CT OS 1 109.500 292.880 ; SUG
F B F 1 109.500 418.400 ; J. Phys. Chem. B
(2004), 108, 12978
; for glucose
CG CG CG 1 112.700 488.273 ; CHARMM 22 parameter file
CG CG HC 1 110.700 313.800 ; CHARMM 22 parameter file
HC CG HC 1 107.800 276.144 ; CHARMM 22 parameter file
CG CG OS 1 109.500 418.400 ;
CG CG OH 1 109.500 418.400 ;
HC CG OH 1 109.500 292.880 ;
CG OH HO 1 108.500 460.240 ;
CG OS CG 1 109.500 502.080 ;
HC CG OS 1 109.500 292.880 ; SUG
OS CG OH 1 111.550 774.876 ; this is taken from OS
CO OH, Ha,CarbRes 180,207(88)Merz,JCC 15,1019 (94)
[ dihedraltypes ]
; i j k l func coefficients
; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form
; according to the formula in the Gromacs manual.
X NA CR X 3 19.46000 0.00000 -19.46000
0.00000 0.00000 0.00000 ; (From wildcard)
X CW CW X 3 44.98000 0.00000 -44.98000
0.00000 0.00000 0.00000 ;
X NA CW X 3 12.55000 0.00000 -12.55000
0.00000 0.00000 0.00000 ;
CW NA CT HC 3 0.25950 0.77850 0.00000
-1.03800 0.00000 0.00000 ; (From wildcard) heterocycles
CR NA CT HC 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ; (From wildcard) heterocycles
CW NA CT CT 3 2.92600 4.76800 -6.10600
-1.58800 0.00000 0.00000 ; (From wildcard) heterocycles
CR NA CT CT 3 -2.63450 2.63450 0.00000
0.00000 0.00000 0.00000 ; imidazoles, indoles, purines
NA CT CT CT 3 -1.17750 1.93550 -3.16400
2.40600 0.00000 0.00000 ; (From wildcard) heterocycles
NA CT CT HC 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ; (From wildcard) heterocycles
CT CT CT HC 3 0.76550 2.29650 0.00000
-3.06200 0.00000 0.00000 ; (From wildcard) heterocycles
HC CT CT HC 3 0.66550 1.99650 0.00000
-2.66200 0.00000 0.00000 ; hydrocarbon *new* 11/99
CT CT CT CT 3 3.56650 -1.88950 0.65700
-2.33400 0.00000 0.00000 ; (From wildcard) heterocycles
X NA X X 3 8.37000 0.00000 -8.37000
0.00000 0.00000 0.00000 ;
X CW X X 3 9.20000 0.00000 -9.20000
0.00000 0.00000 0.00000 ;
X CR X X 3 9.20000 0.00000 -9.20000
0.00000 0.00000 0.00000 ;
HC CT C_3 O2 3 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 ; carboxylate ion
CT OS P O2 3 1.17570 3.52711 0.00000
-4.70281 0.00000 0.00000 ; Me2PO4 (-)
CT OS P OS 3 1.04600 3.13800 10.04160
-4.18400 0.00000 0.00000 ; Me2PO4 (-), from Amber.
HC CT OS P 3 0.74684 2.24053 0.00000
-2.98738 0.00000 0.00000 ; Me2PO4 (-)
; for glucose
CG CG CG CG 3 2.92880 -1.46440 0.20920
-1.67360 0.00000 0.00000 ; hydrocarbon all-atom
CG CG CG HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; hydrocarbon all-atom
HC CG CG HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; hydrocarbon *new* 11/99
CG CG OH HO 3 -0.44350 3.83255 0.72801
-4.11705 0.00000 0.00000 ; alcohols AA
HC CG OH HO 3 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000 ; alcohols AA
CG CG CG OH 3 2.87441 0.58158 2.09200
-5.54799 0.00000 0.00000 ; alcohols, ethers AA
CG CG CG OS 3 2.87441 0.58158 2.09200
-5.54799 0.00000 0.00000 ; alcohols, ethers AA
CG CG OS CG 3 1.71544 2.84512 1.04600
-5.60656 0.00000 0.00000 ; ethers AA
CG OS CG HC 3 1.58992 4.76976 0.00000
-6.35968 0.00000 0.00000 ; ethers AA
CG OS CG OH 3 -5.35761 13.61683 8.44331
-16.70253 0.00000 0.00000 ; acetals AA
HC CG CG OH 3 0.97905 2.93716 0.00000
-3.91622 0.00000 0.00000 ; alcohols, ethers AA
HC CG CG OS 3 0.97905 2.93716 0.00000
-3.91622 0.00000 0.00000 ; alcohols, ethers AA
HC CG OH HO 3 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000 ; alcohols AA
OH CG CG OH 3 18.96607 -18.96607 0.00000
0.00000 0.00000 0.00000 ; hexopyranoses
OH CG CG OS 3 9.03534 -9.03534 0.00000
0.00000 0.00000 0.00000 ; hexopyranoses
HO OH CG OS 3 -10.17967 2.64847 7.55630
-0.02510 0.00000 0.00000 ; hexopyranoses, this is taken from HO OH
CO OS.
; These parameter are checked and corrected on September 22, 2013
; Paramter are from J. Phys. Chem. B. 2008, 112, 5039-5046
; Derived from parsing of runfiles/alat.top.orig
;[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_969 So 16 32.06000 1.180 A 3.55000e-01 1.04600e+00
; SIG
opls_970 Os4 8 15.99940 -0.650 A 3.15000e-01 8.37000e-01
opls_971 Oc4 8 15.99940 -0.450 A 2.90000e-01 5.86000e-01
opls_972 CS4 6 12.01100 0.220 A 3.50000e-01 2.76000e-01
opls_973 CE 6 12.01100 -0.180 A 3.50000e-01 2.76140e-01
opls_974 HS4 1 1.00800 0.00 A 2.50000e-01 1.26000e-01
opls_975 HE 1 1.00800 0.060 A 2.50000e-01 1.25520e-01
[ bondtypes ]
; i j func b0 kb
So Os4 1 0.14550 533100.0
So Oc4 1 0.16330 178960.0
Oc4 CS4 1 0.14020 74583.0
CS4 CE 1 0.15290 224200.0
CS4 HS4 1 0.10900 284500.0
CE HE 1 0.10900 284500.0
[ angletypes ]
; i j k func th0 cth
Os4 So Os4 1 114.000 969.0
Oc4 So Os4 1 103.500 1239.6
CS4 Oc4 So 1 116.600 300.5
HS4 CS4 Oc4 1 109.700 488.7
OC4 CS4 CE 1 107.800 765.6
CE CS4 HS4 1 110.700 313.800
CS4 CE HE 1 110.700 313.800
HS4 CS4 HS4 1 107.800 276.200
HE CE HE 1 107.800 276.200
[ dihedraltypes ]
; i j k l func coefficients
Os4 So Oc4 CS4 3 1.24075 3.72225 0.00000 -4.96300
0.00000 0.00000
So Oc4 CS4 HS4 3 0.84290 2.52870 0.00000 -3.37160
0.00000 0.00000
So Oc4 CS4 CE 3 -5.37335 10.49650 3.11330 -2.98820
0.00000 0.00000
Oc4 CS4 CE HE 3 1.03490 3.10470 0.00000 -4.13960
0.00000 0.00000
HS4 Cs4 CE HE 3 0.66550 1.99650 0.00000 -2.66200
0.00000 0.00000 ; hydrocarbon *new* 11/99
[ moleculetype ]
; Name nrexcl
EMI 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_561 1 EMI C 1 -0.13 12.011 ;
qtot -0.13
2 opls_561 1 EMI C2 2 -0.13 12.011 ;
qtot -0.26
3 opls_557 1 EMI N3 3 0.15 14.0067 ;
qtot -0.11
4 opls_558 1 EMI C4 4 -0.11 12.011 ;
qtot -0.22
5 opls_557 1 EMI N5 5 0.15 14.0067 ;
qtot -0.07
6 opls_136 1 EMI C6 6 -0.05 12.011 ;
qtot -0.12
7 opls_135 1 EMI C7 7 -0.17 12.011 ;
qtot -0.29
8 opls_135 1 EMI C8 8 -0.17 12.011 ;
qtot -0.46
9 opls_564 1 EMI H9 9 0.21 1.008 ;
qtot -0.25
10 opls_564 1 EMI H10 9 0.21 1.008 ;
qtot -0.04
11 opls_563 1 EMI H11 9 0.21 1.008 ;
qtot 0.17
12 opls_140 1 EMI H12 10 0.13 1.008 ;
qtot 0.3
13 opls_140 1 EMI H13 10 0.13 1.008 ;
qtot 0.43
14 opls_140 1 EMI H14 10 0.13 1.008 ;
qtot 0.56
15 opls_140 1 EMI H15 11 0.13 1.008 ;
qtot 0.69
16 opls_140 1 EMI H16 11 0.13 1.008 ;
qtot 0.82
17 opls_140 1 EMI H17 12 0.06 1.008 ;
qtot 0.88
18 opls_140 1 EMI H18 12 0.06 1.008 ;
qtot 0.94
19 opls_140 1 EMI H19 12 0.06 1.008 ;
qtot 1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 5 1
1 9 1
2 3 1
2 10 1
3 4 1
3 8 1
4 5 1
4 11 1
5 6 1
6 7 1
6 15 1
6 16 1
7 17 1
7 18 1
7 19 1
8 12 1
8 13 1
8 14 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 8 1
1 11 1
1 15 1
1 16 1
2 6 1
2 11 1
2 12 1
2 13 1
2 14 1
3 6 1
3 9 1
4 7 1
4 9 1
4 10 1
4 12 1
4 13 1
4 14 1
4 15 1
4 16 1
5 8 1
5 10 1
5 17 1
5 18 1
5 19 1
6 9 1
6 11 1
8 10 1
8 11 1
9 10 1
15 17 1
15 18 1
15 19 1
16 17 1
16 18 1
16 19 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 5 1
2 1 9 1
5 1 9 1
1 2 3 1
1 2 10 1
3 2 10 1
2 3 4 1
2 3 8 1
4 3 8 1
3 4 5 1
3 4 11 1
5 4 11 1
1 5 4 1
1 5 6 1
4 5 6 1
5 6 7 1
5 6 15 1
5 6 16 1
7 6 15 1
7 6 16 1
15 6 16 1
6 7 17 1
6 7 18 1
6 7 19 1
17 7 18 1
17 7 19 1
18 7 19 1
3 8 12 1
3 8 13 1
3 8 14 1
12 8 13 1
12 8 14 1
13 8 14 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
5 1 2 3 3
5 1 2 10 3
9 1 2 3 3
9 1 2 10 3
2 1 5 4 3
2 1 5 6 3
9 1 5 4 3
9 1 5 6 3
1 2 3 4 3
1 2 3 8 3
10 2 3 4 3
10 2 3 8 3
2 3 4 5 3
2 3 4 11 3
8 3 4 5 3
8 3 4 11 3
2 3 8 12 3
2 3 8 13 3
2 3 8 14 3
4 3 8 12 3
4 3 8 13 3
4 3 8 14 3
3 4 5 1 3
3 4 5 6 3
11 4 5 1 3
11 4 5 6 3
1 5 6 7 3
1 5 6 15 3
1 5 6 16 3
4 5 6 7 3
4 5 6 15 3
4 5 6 16 3
5 6 7 17 3
5 6 7 18 3
5 6 7 19 3
15 6 7 17 3
15 6 7 18 3
15 6 7 19 3
16 6 7 17 3
16 6 7 18 3
16 6 7 19 3
;#include "glu-emi_lop-modify.itp"
;#include "dmso-nilesh.itp"
;#include "ffoplsaanb.itp"
;#include "ffoplsaabon.itp"
;#include "pf6_opls.itp"
;#include "solvent.itp"
;#include "bmi1.itp"
;#include "acetate.itp"
;#include "pf6.itp"
[ moleculetype ]
; Name nrexcl
ETS 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_969 1 ETS S20 1 1.18 32.03 ;
qtot 1.18
2 opls_970 1 ETS O21 2 -0.65 15.9994 ;
qtot 0.53
3 opls_970 1 ETS O22 2 -0.65 15.9994 ;
qtot -0.12
4 opls_970 1 ETS O23 2 -0.65 15.9994 ;
qtot -0.77
5 opls_971 1 ETS O24 3 -0.45 15.9994 ;
qtot -1.22
6 opls_972 1 ETS C25 4 0.22 12.011 ;
qtot -1
7 opls_973 1 ETS C26 5 -0.18 12.011 ;
qtot -1.18
8 opls_974 1 ETS H27 6 0 1.008 ;
qtot -1.18
9 opls_974 1 ETS H28 6 0 1.008 ;
qtot -1.18
10 opls_975 1 ETS H29 7 0.06 1.008 ;
qtot -1.12
11 opls_975 1 ETS H30 7 0.06 1.008 ;
qtot -1.06
12 opls_975 1 ETS H31 7 0.06 1.008 ;
qtot -1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
6 7 1
6 8 1
6 9 1
7 10 1
7 11 1
7 12 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 8 1
1 9 1
2 6 1
3 6 1
4 6 1
5 10 1
5 11 1
5 12 1
8 10 1
8 11 1
8 12 1
9 10 1
9 11 1
9 12 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
5 6 7 1
5 6 8 1
5 6 9 1
7 6 8 1
7 6 9 1
8 6 9 1
6 7 10 1
6 7 11 1
6 7 12 1
10 7 11 1
10 7 12 1
11 7 12 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
2 1 5 6 3
3 1 5 6 3
4 1 5 6 3
1 5 6 7 3
1 5 6 8 3
1 5 6 9 3
5 6 7 10 3
5 6 7 11 3
5 6 7 12 3
8 6 7 10 3
8 6 7 11 3
8 6 7 12 3
9 6 7 10 3
9 6 7 11 3
9 6 7 12 3
;#include "water-flexiable.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_561 1 EMI C 1 -0.13 12.011 ;
qtot -0.13
2 opls_561 1 EMI C2 2 -0.13 12.011 ;
qtot -0.26
3 opls_557 1 EMI N3 3 0.15 14.0067 ;
qtot -0.11
4 opls_558 1 EMI C4 4 -0.11 12.011 ;
qtot -0.22
5 opls_557 1 EMI N5 5 0.15 14.0067 ;
qtot -0.07
6 opls_136 1 EMI C6 6 -0.05 12.011 ;
qtot -0.12
7 opls_135 1 EMI C7 7 -0.17 12.011 ;
qtot -0.29
8 opls_135 1 EMI C8 8 -0.17 12.011 ;
qtot -0.46
9 opls_564 1 EMI H9 9 0.21 1.008 ;
qtot -0.25
10 opls_564 1 EMI H10 9 0.21 1.008 ;
qtot -0.04
11 opls_563 1 EMI H11 9 0.21 1.008 ;
qtot 0.17
12 opls_140 1 EMI H12 10 0.13 1.008 ;
qtot 0.3
13 opls_140 1 EMI H13 10 0.13 1.008 ;
qtot 0.43
14 opls_140 1 EMI H14 10 0.13 1.008 ;
qtot 0.56
15 opls_140 1 EMI H15 11 0.13 1.008 ;
qtot 0.69
16 opls_140 1 EMI H16 11 0.13 1.008 ;
qtot 0.82
17 opls_140 1 EMI H17 12 0.06 1.008 ;
qtot 0.88
18 opls_140 1 EMI H18 12 0.06 1.008 ;
qtot 0.94
19 opls_140 1 EMI H19 12 0.06 1.008 ;
qtot 1
20 opls_969 2 ETS S20 13 1.18 32.03 ;
qtot 2.18
21 opls_970 2 ETS O21 14 -0.65 15.9994 ;
qtot 1.53
22 opls_970 2 ETS O22 14 -0.65 15.9994 ;
qtot 0.88
23 opls_970 2 ETS O23 14 -0.65 15.9994 ;
qtot 0.23
24 opls_971 2 ETS O24 15 -0.45 15.9994 ;
qtot -0.22
25 opls_972 2 ETS C25 16 0.22 12.011 ;
qtot 0
26 opls_973 2 ETS C26 17 -0.18 12.011 ;
qtot -0.18
27 opls_974 2 ETS H27 18 0 1.008 ;
qtot -0.18
28 opls_974 2 ETS H28 18 0 1.008 ;
qtot -0.18
29 opls_975 2 ETS H29 19 0.06 1.008 ;
qtot -0.12
30 opls_975 2 ETS H30 19 0.06 1.008 ;
qtot -0.06
31 opls_975 2 ETS H31 19 0.06 1.008 ;
qtot 0
32 opls_561 3 EMI C 20 -0.13 12.011 ;
qtot -0.13
33 opls_561 3 EMI C2 21 -0.13 12.011 ;
qtot -0.26
34 opls_557 3 EMI N3 22 0.15 14.0067 ;
qtot -0.11
35 opls_558 3 EMI C4 23 -0.11 12.011 ;
qtot -0.22
36 opls_557 3 EMI N5 24 0.15 14.0067 ;
qtot -0.07
37 opls_136 3 EMI C6 25 -0.05 12.011 ;
qtot -0.12
38 opls_135 3 EMI C7 26 -0.17 12.011 ;
qtot -0.29
39 opls_135 3 EMI C8 27 -0.17 12.011 ;
qtot -0.46
40 opls_564 3 EMI H9 28 0.21 1.008 ;
qtot -0.25
41 opls_564 3 EMI H10 28 0.21 1.008 ;
qtot -0.04
42 opls_563 3 EMI H11 28 0.21 1.008 ;
qtot 0.17
43 opls_140 3 EMI H12 29 0.13 1.008 ;
qtot 0.3
44 opls_140 3 EMI H13 29 0.13 1.008 ;
qtot 0.43
45 opls_140 3 EMI H14 29 0.13 1.008 ;
qtot 0.56
46 opls_140 3 EMI H15 30 0.13 1.008 ;
qtot 0.69
47 opls_140 3 EMI H16 30 0.13 1.008 ;
qtot 0.82
48 opls_140 3 EMI H17 31 0.06 1.008 ;
qtot 0.88
49 opls_140 3 EMI H18 31 0.06 1.008 ;
qtot 0.94
50 opls_140 3 EMI H19 31 0.06 1.008 ;
qtot 1
51 opls_969 4 ETS S20 32 1.18 32.03 ;
qtot 2.18
52 opls_970 4 ETS O21 33 -0.65 15.9994 ;
qtot 1.53
53 opls_970 4 ETS O22 33 -0.65 15.9994 ;
qtot 0.88
54 opls_970 4 ETS O23 33 -0.65 15.9994 ;
qtot 0.23
55 opls_971 4 ETS O24 34 -0.45 15.9994 ;
qtot -0.22
56 opls_972 4 ETS C25 35 0.22 12.011 ;
qtot 0
57 opls_973 4 ETS C26 36 -0.18 12.011 ;
qtot -0.18
58 opls_974 4 ETS H27 37 0 1.008 ;
qtot -0.18
59 opls_974 4 ETS H28 37 0 1.008 ;
qtot -0.18
60 opls_975 4 ETS H29 38 0.06 1.008 ;
qtot -0.12
61 opls_975 4 ETS H30 38 0.06 1.008 ;
qtot -0.06
62 opls_975 4 ETS H31 38 0.06 1.008 ;
qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 5 1
1 9 1
2 3 1
2 10 1
3 4 1
3 8 1
4 5 1
4 11 1
5 6 1
6 7 1
6 15 1
6 16 1
7 17 1
7 18 1
7 19 1
8 12 1
8 13 1
8 14 1
20 21 1
20 22 1
20 23 1
20 24 1
24 25 1
25 26 1
25 27 1
25 28 1
26 29 1
26 30 1
26 31 1
32 33 1
32 36 1
32 40 1
33 34 1
33 41 1
34 35 1
34 39 1
35 36 1
35 42 1
36 37 1
37 38 1
37 46 1
37 47 1
38 48 1
38 49 1
38 50 1
39 43 1
39 44 1
39 45 1
51 52 1
51 53 1
51 54 1
51 55 1
55 56 1
56 57 1
56 58 1
56 59 1
57 60 1
57 61 1
57 62 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 8 1
1 11 1
1 15 1
1 16 1
2 6 1
2 11 1
2 12 1
2 13 1
2 14 1
3 6 1
3 9 1
4 7 1
4 9 1
4 10 1
4 12 1
4 13 1
4 14 1
4 15 1
4 16 1
5 8 1
5 10 1
5 17 1
5 18 1
5 19 1
6 9 1
6 11 1
8 10 1
8 11 1
9 10 1
15 17 1
15 18 1
15 19 1
16 17 1
16 18 1
16 19 1
20 26 1
20 27 1
20 28 1
21 25 1
22 25 1
23 25 1
24 29 1
24 30 1
24 31 1
27 29 1
27 30 1
27 31 1
28 29 1
28 30 1
28 31 1
32 38 1
32 39 1
32 42 1
32 46 1
32 47 1
33 37 1
33 42 1
33 43 1
33 44 1
33 45 1
34 37 1
34 40 1
35 38 1
35 40 1
35 41 1
35 43 1
35 44 1
35 45 1
35 46 1
35 47 1
36 39 1
36 41 1
36 48 1
36 49 1
36 50 1
37 40 1
37 42 1
39 41 1
39 42 1
40 41 1
46 48 1
46 49 1
46 50 1
47 48 1
47 49 1
47 50 1
51 57 1
51 58 1
51 59 1
52 56 1
53 56 1
54 56 1
55 60 1
55 61 1
55 62 1
58 60 1
58 61 1
58 62 1
59 60 1
59 61 1
59 62 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 5 1
2 1 9 1
5 1 9 1
1 2 3 1
1 2 10 1
3 2 10 1
2 3 4 1
2 3 8 1
4 3 8 1
3 4 5 1
3 4 11 1
5 4 11 1
1 5 4 1
1 5 6 1
4 5 6 1
5 6 7 1
5 6 15 1
5 6 16 1
7 6 15 1
7 6 16 1
15 6 16 1
6 7 17 1
6 7 18 1
6 7 19 1
17 7 18 1
17 7 19 1
18 7 19 1
3 8 12 1
3 8 13 1
3 8 14 1
12 8 13 1
12 8 14 1
13 8 14 1
21 20 22 1
21 20 23 1
21 20 24 1
22 20 23 1
22 20 24 1
23 20 24 1
20 24 25 1
24 25 26 1
24 25 27 1
24 25 28 1
26 25 27 1
26 25 28 1
27 25 28 1
25 26 29 1
25 26 30 1
25 26 31 1
29 26 30 1
29 26 31 1
30 26 31 1
33 32 36 1
33 32 40 1
36 32 40 1
32 33 34 1
32 33 41 1
34 33 41 1
33 34 35 1
33 34 39 1
35 34 39 1
34 35 36 1
34 35 42 1
36 35 42 1
32 36 35 1
32 36 37 1
35 36 37 1
36 37 38 1
36 37 46 1
36 37 47 1
38 37 46 1
38 37 47 1
46 37 47 1
37 38 48 1
37 38 49 1
37 38 50 1
48 38 49 1
48 38 50 1
49 38 50 1
34 39 43 1
34 39 44 1
34 39 45 1
43 39 44 1
43 39 45 1
44 39 45 1
52 51 53 1
52 51 54 1
52 51 55 1
53 51 54 1
53 51 55 1
54 51 55 1
51 55 56 1
55 56 57 1
55 56 58 1
55 56 59 1
57 56 58 1
57 56 59 1
58 56 59 1
56 57 60 1
56 57 61 1
56 57 62 1
60 57 61 1
60 57 62 1
61 57 62 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
5 1 2 3 3
5 1 2 10 3
9 1 2 3 3
9 1 2 10 3
2 1 5 4 3
2 1 5 6 3
9 1 5 4 3
9 1 5 6 3
1 2 3 4 3
1 2 3 8 3
10 2 3 4 3
10 2 3 8 3
2 3 4 5 3
2 3 4 11 3
8 3 4 5 3
8 3 4 11 3
2 3 8 12 3
2 3 8 13 3
2 3 8 14 3
4 3 8 12 3
4 3 8 13 3
4 3 8 14 3
3 4 5 1 3
3 4 5 6 3
11 4 5 1 3
11 4 5 6 3
1 5 6 7 3
1 5 6 15 3
1 5 6 16 3
4 5 6 7 3
4 5 6 15 3
4 5 6 16 3
5 6 7 17 3
5 6 7 18 3
5 6 7 19 3
15 6 7 17 3
15 6 7 18 3
15 6 7 19 3
16 6 7 17 3
16 6 7 18 3
16 6 7 19 3
21 20 24 25 3
22 20 24 25 3
23 20 24 25 3
20 24 25 26 3
20 24 25 27 3
20 24 25 28 3
24 25 26 29 3
24 25 26 30 3
24 25 26 31 3
27 25 26 29 3
27 25 26 30 3
27 25 26 31 3
28 25 26 29 3
28 25 26 30 3
28 25 26 31 3
36 32 33 34 3
36 32 33 41 3
40 32 33 34 3
40 32 33 41 3
33 32 36 35 3
33 32 36 37 3
40 32 36 35 3
40 32 36 37 3
32 33 34 35 3
32 33 34 39 3
41 33 34 35 3
41 33 34 39 3
33 34 35 36 3
33 34 35 42 3
39 34 35 36 3
39 34 35 42 3
33 34 39 43 3
33 34 39 44 3
33 34 39 45 3
35 34 39 43 3
35 34 39 44 3
35 34 39 45 3
34 35 36 32 3
34 35 36 37 3
42 35 36 32 3
42 35 36 37 3
32 36 37 38 3
32 36 37 46 3
32 36 37 47 3
35 36 37 38 3
35 36 37 46 3
35 36 37 47 3
36 37 38 48 3
36 37 38 49 3
36 37 38 50 3
46 37 38 48 3
46 37 38 49 3
46 37 38 50 3
47 37 38 48 3
47 37 38 49 3
47 37 38 50 3
52 51 55 56 3
53 51 55 56 3
54 51 55 56 3
51 55 56 57 3
51 55 56 58 3
51 55 56 59 3
55 56 57 60 3
55 56 57 61 3
55 56 57 62 3
58 56 57 60 3
58 56 57 61 3
58 56 57 62 3
59 56 57 60 3
59 56 57 61 3
59 56 57 62 3
; Include Position restraint file
; Include water topology
;#include "spc.itp"
; Include generic topology for ions
;#include "ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
EMI 2
ETS 2
Nilesh
> On 9/22/13 7:13 PM, Nilesh Dhumal wrote:
>> Hello,
>>
>> I am doing energy minimization for my system. I am getting following
>> warnings
>>
>> Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20)
>> Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21)
>> Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22)
>> Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23)
>> Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24)
>> Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25)
>> Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26)
>> Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27)
>> Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28)
>> Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29)
>> Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30)
>> Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31)
>> Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C)
>> Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2)
>> Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3)
>> Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4)
>> Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5)
>> Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6)
>> Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7)
>> Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8)
>>
>>
>> Here is .pdb file
>>
>> TITLE Protein
>> REMARK THIS IS A SIMULATION BOX
>> CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1
>> MODEL 1
>> ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00
>> ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00
>> ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00
>> ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00
>> ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00
>> ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00
>> ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00
>> ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00
>> ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00
>> ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00
>> ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00
>> ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00
>> ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00
>> ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00
>> ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00
>> ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00
>> ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00
>> ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00
>> ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00
>> ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00
>> ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00
>> ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00
>> ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00
>> ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00
>> ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00
>> ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00
>> ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00
>> ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00
>> ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00
>> ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00
>> ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00
>> ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00
>> ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00
>>
>> and .top file is
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass
>> typeB
>> chargeB massB
>> 1 opls_561 1 EMI C 1 -0.13 12.011 ;
>> qtot -0.13
>> 2 opls_561 1 EMI C2 2 -0.13 12.011 ;
>> qtot -0.26
>> 3 opls_557 1 EMI N3 3 0.15 14.0067 ;
>> qtot -0.11
>> 4 opls_558 1 EMI C4 4 -0.11 12.011 ;
>> qtot -0.22
>> 5 opls_557 1 EMI N5 5 0.15 14.0067 ;
>> qtot -0.07
>> 6 opls_136 1 EMI C6 6 -0.05 12.011 ;
>> qtot -0.12
>> 7 opls_135 1 EMI C7 7 -0.17 12.011 ;
>> qtot -0.29
>> 8 opls_135 1 EMI C8 8 -0.17 12.011 ;
>> qtot -0.46
>> 9 opls_564 1 EMI H9 9 0.21 1.008 ;
>> qtot -0.25
>> 10 opls_564 1 EMI H10 9 0.21 1.008 ;
>> qtot -0.04
>> 11 opls_563 1 EMI H11 9 0.21 1.008 ;
>> qtot 0.17
>> 12 opls_140 1 EMI H12 10 0.13 1.008 ;
>> qtot 0.3
>> 13 opls_140 1 EMI H13 10 0.13 1.008 ;
>> qtot 0.43
>> 14 opls_140 1 EMI H14 10 0.13 1.008 ;
>> qtot 0.56
>> 15 opls_140 1 EMI H15 11 0.13 1.008 ;
>> qtot 0.69
>> 16 opls_140 1 EMI H16 11 0.13 1.008 ;
>> qtot 0.82
>> 17 opls_140 1 EMI H17 12 0.06 1.008 ;
>> qtot 0.88
>> 18 opls_140 1 EMI H18 12 0.06 1.008 ;
>> qtot 0.94
>> 19 opls_140 1 EMI H19 12 0.06 1.008 ;
>> qtot 1
>> 20 opls_969 2 ETS S20 13 1.18 32.03 ;
>> qtot 2.18
>> 21 opls_970 2 ETS O21 14 -0.65 15.9994 ;
>> qtot 1.53
>> 22 opls_970 2 ETS O22 14 -0.65 15.9994 ;
>> qtot 0.88
>> 23 opls_970 2 ETS O23 14 -0.65 15.9994 ;
>> qtot 0.23
>> 24 opls_971 2 ETS O24 15 -0.45 15.9994 ;
>> qtot -0.22
>> 25 opls_972 2 ETS C25 16 0.22 12.011 ;
>> qtot 0
>> 26 opls_973 2 ETS C26 17 -0.18 12.011 ;
>> qtot -0.18
>> 27 opls_974 2 ETS H27 18 0 1.008 ;
>> qtot -0.18
>> 28 opls_974 2 ETS H28 18 0 1.008 ;
>> qtot -0.18
>> 29 opls_975 2 ETS H29 19 0.06 1.008 ;
>> qtot -0.12
>> 30 opls_975 2 ETS H30 19 0.06 1.008 ;
>> qtot -0.06
>> 31 opls_975 2 ETS H31 19 0.06 1.008 ;
>> qtot 0
>>
>>
>> Could you tell why am I getting this warnings? I am using VERSION 4.0.7
>> .
>>
>
> The [molecules] section of the topology is out of order with respect to
> the
> atoms in the coordinate file. In the absence of the full .top (and any
> relevant
> .itp files) and coordinate file, there's not much more to guess at. The
> error
> shows you that grompp expects an "ETS" residue to have started, but it's
> finding
> atoms belonging to an "EMI" residue.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
> --
> gmx-users mailing list gmx-users@gromacs.org
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