[gmx-users] RENUMTOP

Martina Bertsch, PhD mbe404 at lulu.it.northwestern.edu
Sun Feb 15 00:41:01 CET 2004


I need to perform simulated annealing of the receptor-ligand complex in 
vacuum as described in my previous e-mails.

I prepared the rec.gro and rec.top using pdb2gmx by selecting ffG43b1. I 
also prepared the lig_vac.itp manually using the ffG43a1 parameters, as 
the PRODRG server only outputs the ffgmx itp. The lig_vac.itp is enclosed.

Next, I merged the rec.top and lig_vac.itp into one file, rec_lig.top, 
as described in Anton's e-mail, dated December 1, 2003:

1) I labeled all lig atom numbers (in atoms, bonds, angles, etc) with an 'm' after the atom numbers.
2) I merged all sections separately (i.e., appended lig atoms to protein atoms, lig bonds to protein bonds, etc).
3) I ran the 'renumtop' script on the merged topology; it did re-assign the right atom numbers (in atoms, bonds, angles, etc) for all lig
   atoms added in step 2.

However, when I ran grompp with the new merged and renumbered top file, I got the following message:

Fatal error: Invalid bond type 0

I suspect I am missing something in my lig_vac.itp, but I am completely new to building ffG43a1/b1 ligand itp files "from scratch". 

Any help will be greatly appreciated.

Best regards,
Martina Bertsch, Ph.D.

 [ moleculetype ]
 ;name nrexcl
DRG      3
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  
typeB    chargeB     massB
    1m       CH3     285   DRG     CAO      1       0.000    15.035
    2m         C     285   DRG     CAM      1       0.380    12.011
    3m         O     285   DRG     OAN      1      -0.380   15.9994
    4m         N     285   DRG     NAL      2      -0.280   14.0067
    5m         H     285   DRG     HAB      2       0.280     1.008
    6m       CH2     285   DRG     CAK      3       0.000    14.027
    7m       CH2     285   DRG     CAJ      3       0.000    14.027
    8m         C     285   DRG     CAA      4      -0.140    12.011
    9m         C     285   DRG     CAC      4       0.000    12.011
   10m       CR1     285   DRG     CAF      5       0.000    13.019
   11m         C     285   DRG     CAH      5       0.100    12.011
   12m        OA     285   DRG     OAP      6      -0.100   15.9994
   13m       CH3     285   DRG     CAQ      6       0.000    15.035
   14m       CR1     285   DRG     CAI      7       0.000    13.019
   15m       CR1     285   DRG     CAG      7       0.000    13.019
   16m         C     285   DRG     CAE      8       0.000    12.011
   17m        NR     285   DRG     NAD      8      -0.050   14.0067
   18m         H     285   DRG     HAA      8       0.190     1.008
   19m       CR1     285   DRG     CAB      8       0.000    13.019
[ bonds ]
  1m   2m    gb_26
  2m   3m    gb_4
  2m   4m    gb_9
  4m   5m    gb_2
  4m   6m    gb_20
  6m   7m    gb_26
  7m   8m    gb_14
  8m   19m    gb_9
  8m   9m    gb_9
  19m   17m    gb_9
  17m   18m    gb_2
  17m   16m    gb_9
  16m   9m    gb_15
  9m   10m    gb_15
  10m   11m    gb_15
  11m   14m    gb_15
  14m   15m    gb_15
  15m   16m    gb_15
  11m   12m    gb_12
  12m   13m    gb_17
 [ angles ]
;   ai    aj    ak  gromos type
  1m   2m   3m    ga_29
  1m   2m   4m    ga_18
  3m   2m   4m    ga_32
  2m   4m   5m    ga_31
  2m   4m   6m    ga_30
  5m   4m   6m    ga_17
  4m   6m   7m    ga_12
  6m   7m   8m    ga_14
  7m   8m   19m    ga_36
  8m   19m   17m    ga_6
  19m   17m   18m    ga_35
  19m   17m   16m    ga_6
  19m   8m   9m    ga_6
  8m   9m   16m    ga_6
  9m   16m   17m    ga_6
  17m   16m   15m    ga_38
  8m   9m   10m    ga_38
  16m   9m   10m    ga_26
  9m   10m   11m    ga_26
  10m   11m   14m    ga_26
  11m   14m   15m    ga_26
  14m   15m   16m    ga_26
  15m   16m   9m    ga_26
  10m   11m   12m    ga_18
  11m   12m   13m    ga_11
  14m   11m   12m    ga_18
 [ impropers ]
;   ai    aj    ak    al  gromos type
  2m   1m   4m   3m    gi_1
  4m   2m   5m   6m    gi_1
  8m   19m   9m   7m    gi_1
  9m   8m   16m   10m    gi_1
  11m   14m   12m   10m    gi_1
  16m   9m   15m   17m    gi_1
  17m   16m   18m   19m    gi_1
  8m   9m   16m   17m    gi_1
  9m   16m   17m   19m    gi_1
  16m   17m   19m   8m    gi_1
  17m   19m   8m   9m    gi_1
  19m   8m   9m   16m    gi_1
  9m   10m   11m   14m    gi_1
  10m   11m   14m   15m    gi_1
  11m   14m   15m   16m    gi_1
  14m   15m   16m   9m    gi_1
  15m   16m   9m   10m    gi_1
  16m   9m   10m   11m    gi_1
 [ dihedrals ]
;   ai    aj    ak    al  gromos type
  1m   2m   4m   6m    gd_4
  7m   6m   4m   2m    gd_19
  8m   7m   6m   4m    gd_17
  19m   8m   7m   6m    gd_20
  10m   11m   12m   13m    gd_2

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