[gmx-users] Hydrogens missing during parameterization
XAvier Periole
x.periole at rug.nl
Wed Apr 14 11:55:16 CEST 2010
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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