[gmx-users] topology file construction
abhisek Mondal
abhisek.mndl at gmail.com
Sun Mar 19 15:02:28 CET 2017
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.mndl at 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*
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