[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Mon Sep 23 01:13:30 CEST 2013
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 .
Thanks
Nilesh
More information about the gromacs.org_gmx-users
mailing list