Hi XAvier,<br><br>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?<br>
Thanks again.<br><br>Regards,<br><br>Anirban<br><br><br><div class="gmail_quote">On Wed, Apr 14, 2010 at 3:50 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style=""><div><br></div>You have the proper itp file for the GROMOS FF. Some H are not explicitly <div>
described!</div><div><div></div><div class="h5"><div><br><div><div>On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote:</div><br><blockquote type="cite">Hi, XAvier,<br><br>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?<br>
Any suggestion is welcome. Thanks a lot for the prompt reply.<br><br>Regards,<br><br>Anirban<br><br><div class="gmail_quote">On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br> You are missing HB1 and HB2, not HB2 and HB3 :))<br> <br> This is due to the force field our are using. Gromos I presume: it<br>
uses the united H idea: non-polar H are not explicitly modeled.<br> <br> you should be able to erase those from your gro file, but I would<br> suggest you get into some literature about the FF you use.<br> <br> XAvier.<div>
<div></div><div><br> <br> On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote:<br> <br> </div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div> Hi ALL,<br> <br> I have a ligand LDOPA with 25 atoms (including all hydrogens).:<br> -------------------------------------------------------------------------------------------------------------------------------------------<br>
DAH COORDS<br> 25<br> 1DAH O 1 5.988 5.216 9.128<br> 1DAH C 2 5.980 5.110 9.194<br> 1DAH OXT 3 5.951 4.985 9.139<br> 1DAH CA 4 6.001 5.107 9.349<br> 1DAH HA 5 5.935 5.027 9.384<br>
1DAH N 6 6.140 5.064 9.387<br> 1DAH H2 7 6.161 4.977 9.343<br> 1DAH H3 8 6.137 5.056 9.486<br> 1DAH H1 9 6.206 5.133 9.356<br> 1DAH CB 10 5.952 5.236 9.422<br>
1DAH HB1 11 5.985 5.320 9.362<br> 1DAH HB2 12 5.999 5.231 9.520<br> 1DAH CG 13 5.802 5.258 9.450<br> 1DAH CD2 14 5.761 5.333 9.565<br> 1DAH HD2 15 5.836 5.375 9.632<br>
1DAH CE2 16 5.623 5.353 9.592<br> 1DAH OE2 17 5.589 5.425 9.704<br> 1DAH HE2 18 5.672 5.454 9.752<br> 1DAH CZ 19 5.523 5.297 9.503<br> 1DAH OZ 20 5.387 5.314 9.525<br>
1DAH HZ 21 5.335 5.268 9.453<br> 1DAH CE1 22 5.564 5.223 9.389<br> 1DAH HE1 23 5.489 5.181 9.321<br> 1DAH CD1 24 5.701 5.203 9.362<br> 1DAH HD1 25 5.731 5.146 9.274<br>
1.02033 1.02033 1.02033<br> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> <br> 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:<br>
<br> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> DAH 3<br> <br> [ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br> 1 OM 1 DAH O 1 -0.715 15.9994<br> 2 C 1 DAH C 1 0.387 12.0110<br> 3 OM 1 DAH OXT 1 -0.716 15.9994<br>
4 CH1 1 DAH CA 1 0.178 13.0190<br> 5 NL 1 DAH N 1 0.683 14.0067<br> 6 H 1 DAH H2 1 0.010 1.0080<br> 7 H 1 DAH H3 1 0.010 1.0080<br>
8 H 1 DAH H1 1 0.011 1.0080<br> 9 CH2 1 DAH CB 1 0.152 14.0270<br> 10 C 1 DAH CG 2 -0.020 12.0110<br> 11 CR1 1 DAH CD2 2 0.001 12.0110<br>
12 HC 1 DAH HD2 2 0.019 1.0080<br> 13 C 1 DAH CE2 3 0.130 12.0110<br> 14 OA 1 DAH OE2 3 -0.197 15.9994<br> 15 H 1 DAH HE2 3 0.051 1.0080<br>
16 C 1 DAH CZ 3 0.130 12.0110<br> 17 OA 1 DAH OZ 3 -0.197 15.9994<br> 18 H 1 DAH HZ 3 0.051 1.0080<br> 19 CR1 1 DAH CE1 3 0.001 12.0110<br>
20 HC 1 DAH HE1 3 0.031 1.0080<br> 21 CR1 1 DAH CD1 4 0.000 12.0110<br> 22 HC 1 DAH HD1 4 0.000 1.0080<br> <br> [ bonds ]<br> ----------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
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.<br>
Thanks a lot in advance.<br> <br> Regards,<br> <br> Anirban<br></div></div> -- <br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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