[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Justin Lemkul
jalemkul at vt.edu
Mon Sep 23 02:34:54 CEST 2013
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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