[gmx-users] Hydrogens missing during parameterization
XAvier Periole
x.periole at rug.nl
Wed Apr 14 12:55:06 CEST 2010
Well, ffG43a2 is a GROMOS FF too! So look at the topology and you'll
see that
it also misses some NON_POLAR hydrogens. You probably generated you itp
file using pdb2gmx and got a gro file with it. Then the absence of H
did not
appear!
The H that are involved in H-bonding are explicitly represented in
GROMOS FF.
The ones that are united are the NON-POLAR ones, typically in CH3/CH2
and CH
groups! Check the ffG43a2.rtp file, it contains residues topologies ...
Again I would suggest you get into some literature before going on.
One day
reading some papers on the GROMOS FF would be instructive :))
XAvier.
On Apr 14, 2010, at 12:28 PM, Anirban Ghosh wrote:
> Hi XAvier,
>
> Thanks for the reply. Actually I want to use this ligand with a
> protein and run the complex using ffG43a2 force-field of
> GROMACS4.0.7. So is it correct to leave away those 3 hydrogens HA,
> HB1 and HB2, which are not explicitly described? Because in protein-
> ligand complexes, hydrogen bond formations between the ligand and
> the protein are important? So should I continue with this .itp file
> with 3 less hydrogens?
> Thanks again.
>
> Regards,
>
> Anirban
>
>
> On Wed, Apr 14, 2010 at 3:50 PM, XAvier Periole <x.periole at rug.nl>
> wrote:
>
> 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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