[gmx-users] topology file construction

[abhisek Mondal]

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*