Hi, I'm using following topology configuration for the above said heteroatom:
1 OM 1 ANP O1G 1 -0.348 15.9994 2 P 1 ANP PG 1 0.971 30.9738 3 OM 1 ANP O2G 1 -0.348 15.9994 4 OM 1 ANP O3G 1 -0.348 15.9994 5 NL 1 ANP N3B 1 -0.275 14.0067 6 H 1 ANP H3B 1 0.398 1.0080 7 P 1 ANP PB 2 0.971 30.9738 8 OM 1 ANP O1B 2 -0.348 15.9994 9 OM 1 ANP O2B 2 -0.348 15.9994 10 OA 1 ANP O3A 3 -0.348 15.9994 11 P 1 ANP PA 3 0.971 30.9738 12 OM 1 ANP O1A 3 -0.348 15.9994 13 OM 1 ANP O2A 3 -0.348 15.9994 14 OA 1 ANP O5' 3 -0.348 15.9994 ;' 15 CH2 1 ANP C5' 4 0.000 14.0270 ;' 16 CH1 1 ANP C4' 4 0.000 13.0190 ;' 17 OA 1 ANP O4' 4 -0.348 15.9994 ;' 18 CH1 1 ANP C3' 5 0.000 13.0190 ;' 19 OA 1 ANP O3' 5 -0.348 15.9994 ;' 20 H 1 ANP H8L 5 0.398 1.0080 21 CH1 1 ANP C2' 5 0.000 13.0190 ;' 22 OA 1 ANP O2' 5 -0.348 15.9994 ;' 23 H 1 ANP H8M 5 0.398 1.0080 24 CH1 1 ANP C1' 5 0.000 13.0190 ;' 25 NR 1 ANP N9 6 -0.275 14.0067 26 CR1 1 ANP C8 6 -0.100 12.0110 27 HC 1 ANP H8 6 0.100 1.0080 28 NR 1 ANP N7 6 -0.275 14.0067 29 C 1 ANP C5 6 0.150 12.0110 30 C 1 ANP C4 7 0.150 12.0110 31 NR 1 ANP N3 7 -0.275 14.0067 32 CR1 1 ANP C2 7 -0.100 12.0110 33 HC 1 ANP H2 7 0.100 1.0080 34 NR 1 ANP N1 7 -0.275 14.0067 35 C 1 ANP C6 7 0.150 12.0110 36 NT 1 ANP N6 7 -0.275 14.0067 37 H 1 ANP H62 7 0.398 1.0080 38 H 1 ANP H61 7 0.398 1.0080 But even after I neutralize the charge using: *grompp_mpi -f em.mdp -c solv.gro -p topol.top -o ions.tpr* *genion_mpi -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1* It says the following when I ran *grompp_mpi -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr* : NOTE 1 [file topol.top, line 10075]: System has non-zero total charge: -0.472999 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Can you please help me out here ? Although the equilibration is running but is it alright to go with it ? On Sun, Mar 19, 2017 at 12:45 PM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > I'm trying to perform a protein-ligand MD run. But could not being > able to construct a reliable topology file of the ligand. I've tried the > PRODRG server but charges comes out so messed up. If I set uniform charges > to same kind of atoms then also how can I validate if my ligand is reliable > one ? > I also tried to use ATB server but it fails every time to converge the > calculations. > > > Can you guys please help me out here with the topology? > > REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 1001 > > REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP B 1001 > > REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP C 1001 > > REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP D 1001 > > REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP E 1001 > > REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP F 1001 > > HET ANP A1001 31 > > HET ANP B1001 31 > > HET ANP C1001 31 > > HET ANP D1001 31 > > HET ANP E1001 31 > > HET ANP F1001 31 > > HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER > > FORMUL 7 ANP 6(C10 H17 N6 O12 P3) > > HETATM 7720 PG ANP F1001 -18.382 -33.045 2.669 0.95 66.72 > P > HETATM 7721 O1G ANP F1001 -17.568 -32.425 1.513 0.95 49.78 > O > HETATM 7722 O2G ANP F1001 -17.436 -33.484 3.882 0.95 45.80 > O > HETATM 7723 O3G ANP F1001 -19.503 -32.058 3.152 0.95 56.32 > O > HETATM 7724 PB ANP F1001 -20.192 -35.263 2.825 0.95 64.11 > P > HETATM 7725 O1B ANP F1001 -21.230 -35.810 1.815 0.95 59.42 > O > HETATM 7726 O2B ANP F1001 -19.412 -36.449 3.483 0.95 56.21 > O > HETATM 7727 N3B ANP F1001 -19.105 -34.396 1.985 0.95 56.88 > N > HETATM 7728 PA ANP F1001 -22.193 -34.728 4.706 0.95 33.39 > P > HETATM 7729 O1A ANP F1001 -22.181 -36.311 4.784 0.95 40.97 > O > HETATM 7730 O2A ANP F1001 -22.096 -34.151 6.101 0.95 36.44 > O > HETATM 7731 O3A ANP F1001 -20.911 -34.311 3.863 0.95 45.79 > O > HETATM 7732 O5' ANP F1001 -23.552 -34.146 3.975 0.95 42.40 > O > HETATM 7733 C5' ANP F1001 -24.895 -34.491 4.338 0.95 34.02 > C > HETATM 7734 C4' ANP F1001 -25.758 -34.185 3.277 0.95 33.40 > C > HETATM 7735 O4' ANP F1001 -26.117 -32.735 3.076 0.95 39.92 > O > HETATM 7736 C3' ANP F1001 -25.120 -34.625 1.876 0.95 40.14 > C > HETATM 7737 O3' ANP F1001 -26.229 -35.409 1.239 0.95 39.00 > O > HETATM 7738 C2' ANP F1001 -24.896 -33.618 1.239 0.95 40.45 > C > HETATM 7739 O2' ANP F1001 -25.295 -33.827 -0.228 0.95 45.29 > O > HETATM 7740 C1' ANP F1001 -25.728 -32.365 1.891 0.95 36.77 > C > HETATM 7741 N9 ANP F1001 -24.830 -31.341 2.101 0.95 38.38 > N > HETATM 7742 C8 ANP F1001 -23.632 -31.145 2.617 0.95 38.60 > C > HETATM 7743 N7 ANP F1001 -23.365 -29.832 2.507 0.95 36.80 > N > HETATM 7744 C5 ANP F1001 -24.405 -29.216 1.924 0.95 35.67 > C > HETATM 7745 C6 ANP F1001 -24.583 -27.858 1.605 0.95 39.88 > C > HETATM 7746 N6 ANP F1001 -23.686 -26.775 1.821 0.95 32.70 > N > HETATM 7747 N1 ANP F1001 -25.707 -27.457 1.021 0.95 39.57 > N > HETATM 7748 C2 ANP F1001 -26.684 -28.394 0.740 0.95 37.40 > C > HETATM 7749 N3 ANP F1001 -26.523 -29.729 1.044 0.95 34.97 > N > HETATM 7750 C4 ANP F1001 -25.347 -30.137 1.658 0.95 37.09 > C > > > > Thanks > -- > Abhisek Mondal > > *Research Fellow* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *INDIA* > -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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