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 <[email protected]> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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