[gmx-users] Hydrogens missing during parameterization

XAvier Periole x.periole at rug.nl
Wed Apr 14 12:20:02 CEST 2010


You have the proper itp file for the GROMOS FF. Some H are not  
explicitly
described!

On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote:

> Hi, XAvier,
>
> Sorry for that mistake. Yes, exactly PRODRG is not giving the non- 
> polar hydrogens. There I am using the GROMOS96.1 FF. So is there any  
> way to get the proper .itp file? I mean any other online server like  
> PRODRG? Or How can I derive the proper .itp file manually?
> Any suggestion is welcome. Thanks a lot for the prompt reply.
>
> Regards,
>
> Anirban
>
> On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole <x.periole at rug.nl>  
> wrote:
>
> You are missing HB1 and HB2, not HB2 and HB3 :))
>
> This is due to the force field our are using. Gromos I presume: it
> uses the united H idea: non-polar H are not explicitly modeled.
>
> you should be able to erase those from your gro file, but I would
> suggest you get into some literature about the FF you use.
>
> XAvier.
>
>
> On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote:
>
> Hi ALL,
>
> I have a ligand LDOPA with 25 atoms (including all hydrogens).:
> -------------------------------------------------------------------------------------------------------------------------------------------
> DAH COORDS
>   25
>    1DAH  O        1   5.988   5.216   9.128
>    1DAH  C        2   5.980   5.110   9.194
>    1DAH  OXT      3   5.951   4.985   9.139
>    1DAH  CA       4   6.001   5.107   9.349
>    1DAH  HA       5   5.935   5.027   9.384
>    1DAH  N        6   6.140   5.064   9.387
>    1DAH  H2       7   6.161   4.977   9.343
>    1DAH  H3       8   6.137   5.056   9.486
>    1DAH  H1       9   6.206   5.133   9.356
>    1DAH  CB      10   5.952   5.236   9.422
>    1DAH  HB1     11   5.985   5.320   9.362
>    1DAH  HB2     12   5.999   5.231   9.520
>    1DAH  CG      13   5.802   5.258   9.450
>    1DAH  CD2     14   5.761   5.333   9.565
>    1DAH  HD2     15   5.836   5.375   9.632
>    1DAH  CE2     16   5.623   5.353   9.592
>    1DAH  OE2     17   5.589   5.425   9.704
>    1DAH  HE2     18   5.672   5.454   9.752
>    1DAH  CZ      19   5.523   5.297   9.503
>    1DAH  OZ      20   5.387   5.314   9.525
>    1DAH  HZ      21   5.335   5.268   9.453
>    1DAH  CE1     22   5.564   5.223   9.389
>    1DAH  HE1     23   5.489   5.181   9.321
>    1DAH  CD1     24   5.701   5.203   9.362
>    1DAH  HD1     25   5.731   5.146   9.274
>   1.02033   1.02033   1.02033
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>  I derived the topology file from PRODRG server. However the .itp  
> file is giving only 22 atoms definition and 3 of the hydrogen atoms  
> are missing:
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> DAH      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>     1        OM     1  DAH       O     1   -0.715  15.9994
>     2         C     1  DAH       C     1    0.387  12.0110
>     3        OM     1  DAH     OXT     1   -0.716  15.9994
>     4       CH1     1  DAH      CA     1    0.178  13.0190
>     5        NL     1  DAH       N     1    0.683  14.0067
>     6         H     1  DAH      H2     1    0.010   1.0080
>     7         H     1  DAH      H3     1    0.010   1.0080
>     8         H     1  DAH      H1     1    0.011   1.0080
>     9       CH2     1  DAH      CB     1    0.152  14.0270
>    10         C     1  DAH      CG     2   -0.020  12.0110
>    11       CR1     1  DAH     CD2     2    0.001  12.0110
>    12        HC     1  DAH     HD2     2    0.019   1.0080
>    13         C     1  DAH     CE2     3    0.130  12.0110
>    14        OA     1  DAH     OE2     3   -0.197  15.9994
>    15         H     1  DAH     HE2     3    0.051   1.0080
>    16         C     1  DAH      CZ     3    0.130  12.0110
>    17        OA     1  DAH      OZ     3   -0.197  15.9994
>    18         H     1  DAH      HZ     3    0.051   1.0080
>    19       CR1     1  DAH     CE1     3    0.001  12.0110
>    20        HC     1  DAH     HE1     3    0.031   1.0080
>    21       CR1     1  DAH     CD1     4    0.000  12.0110
>    22        HC     1  DAH     HD1     4    0.000   1.0080
>
> [ bonds ]
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
> So you can see that HA, HB2 and HB3 hydrogens are missing here. So I  
> am getting error messages popped by grompp commands. How can I get  
> the definition of those missing 3 H atoms? Is it ok if I delete  
> those 3 H atoms from my .gro file and proceed? If not then how to  
> derive parameters for them? Any suggestion is welcome.
> Thanks a lot in advance.
>
> Regards,
>
> Anirban
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