[gmx-users] Residue 'HO4' not found in residue topology database

[Mark Abraham]

On 26/02/2012 10:08 PM, shilpa yadahalli wrote:
> Dear gmx-users,
>
> I am using  CHARMM27 all-atom force field (with CMAP) - version 2.0 
> force field with gromacs 4.5.2 version.
> I want to retain my crystal waters in pdb file. I wrote crystal water 
> according to the same convention when gromacs solvates protein molecule.
> last pat of pdb looks like:
> ATOM   1459  CA  LEU A  94       9.264  -6.783   6.273  0.0700 2.2750
> ATOM   1460  C   LEU A  94       9.604  -7.603   5.021  0.3400 2.0000
> ATOM   1461  OT1 LEU A  94      10.488  -7.171   4.243 -0.6700 1.7000
> ATOM   1462  CB  LEU A  94       9.865  -7.422   7.524 -0.1800 2.1750
> ATOM   1463  CG  LEU A  94      11.295  -7.028   7.888 -0.0900 2.2750
> ATOM   1464  CD1 LEU A  94      11.525  -5.554   7.645 -0.2700 2.0600
> ATOM   1465  CD2 LEU A  94      11.541  -7.378   9.338 -0.2700 2.0600
> ATOM   1466  OT2 LEU A  94       9.160  -8.652   4.607 -0.6700 1.7000
> ATOM   1478  OW  SOL A  95      10.102  -4.251  13.943 -0.8340 1.7682
> ATOM   1479  HW1 SOL A  95      11.032  -3.906  14.073  0.4170 0.2245
> ATOM   1480  HW2 SOL A  95       9.584  -4.002  14.761  0.4170 0.2245
> ATOM   1481  OW  SOL A  96       1.041  -4.800   4.090 -0.8340 1.7682
> ATOM   1482  HW1 SOL A  96       0.661  -4.642   5.002  0.4170 0.2245
> ATOM   1483  HW2 SOL A  96       1.894  -4.299   3.947  0.4170 0.2245
> ATOM   1484  OW  SOL A  97      -0.433   3.575  23.826 -0.8340 1.7682
> ATOM   1485  HW1 SOL A  97       0.247   2.969  23.412  0.4170 0.2245
> ATOM   1486  HW2 SOL A  97      -1.278   3.091  24.054  0.4170 0.2245
>
> I used reference (http://pubs.acs.org/doi/full/10.1021/ct900549r ) 
> that its better to use TIP4-point water model with CHARMM. But it 
> gives me following fatal error:
> Residue 'HO4' not found in residue topology database
> But there is not such atom in my input file. I do not get such error 
> if I'm using TIP3P water model.
> Also, If i delete crystal water molecules, and use TIP4P, then it 
> doens't give me any error (but i dnt water to delete crystal water 
> molecule)

pdb2gmx TIP4P support for CHARMM was mysteriously removed shortly before 
4.5.2 in commit 73b6d63

You can try adding the following to your aminoacids.rtp

Mark

[ HO4 ]
; TIP4P
  [ atoms ]
        OW      OWT4    0.00    0
        HW1     HWT4    0.52    0
        HW2     HWT4    0.52    0
        MW      MWT4    -1.04   0
  [ bonds ]
        OW      HW1
        OW      HW2

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