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.peri...@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.peri...@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 >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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