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Hi, David.<br>
<br>
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<pre wrap=""><br>Next, I merged the rec.top and lig_vac.itp into one file, rec_lig.top, <br>as described in Anton's e-mail, dated December 1, 2003:<br>...<br></pre>
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<pre wrap=""><!---->why? is there a covalent bond between your ligand and protein? otherwise<br>this is not necessary at all. <br></pre>
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I used 'renumtop' because when I just put an #include lig_vac.itp statement
after the #include ffG43b1 line in the top file (made by the pdb2gmx for
the protein), I got the warning from grompp that "the topology is not renumbered
from 1". I have never seen this message before, but I remembered Anton mentioning
'renumtop', so I thought that was somehow specific to ffG43a1/b1. <br>
<blockquote type="cite" cite="mid:1076822955.20123.1.camel@h25n2fls34o1123.telia.com">
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<pre wrap="">However, when I ran grompp with the new merged and renumbered top file, I got the following message:<br><br>Fatal error: Invalid bond type 0<br><br>I suspect I am missing something in my lig_vac.itp, but I am completely new to building ffG43a1/b1 ligand itp files "from scratch". <br></pre>
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<pre wrap=""><!---->Doesn't it say on which line in the topology things go wrong?<br><br>The simplest test for your topology is to minimize the ligand separately<br>of the protein, and in the process get rid of possible error in your<br>ligand top.</pre>
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No, there is no line number in the error message.<br>
<br>
My ligand resembles tryptophan a little bit, so I borrowed some ffG43a1 parameters
for Trp. I will try minimizing the ligand itself. But, is there anything
wrong with the format of my lig_vac.itp?
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<pre wrap=""><br><br><br>Best regards,<br>Martina Bertsch, Ph.D.<br><br> [ moleculetype ]<br> ;name nrexcl<br>DRG 3<br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass <br>typeB chargeB massB<br> 1m CH3 285 DRG CAO 1 0.000 15.035<br> 2m C 285 DRG CAM 1 0.380 12.011<br> 3m O 285 DRG OAN 1 -0.380 15.9994<br> 4m N 285 DRG NAL 2 -0.280 14.0067<br> 5m H 285 DRG HAB 2 0.280 1.008<br> 6m CH2 285 DRG CAK 3 0.000 14.027<br> 7m CH2 285 DRG CAJ 3 0.000 14.027<br> 8m C 285 DRG CAA 4 -0.140 12.011<br> 9m C 285 DRG CAC 4 0.000 12.011<br> 10m CR1 285 DRG CAF 5 0.000 13.019<br> 11m C 285
DRG CAH 5 0.100 12.011<br> 12m OA 285 DRG OAP 6 -0.100 15.9994<br> 13m CH3 285 DRG CAQ 6 0.000 15.035<br> 14m CR1 285 DRG CAI 7 0.000 13.019<br> 15m CR1 285 DRG CAG 7 0.000 13.019<br> 16m C 285 DRG CAE 8 0.000 12.011<br> 17m NR 285 DRG NAD 8 -0.050 14.0067<br> 18m H 285 DRG HAA 8 0.190 1.008<br> 19m CR1 285 DRG CAB 8 0.000 13.019<br>[ bonds ]<br> 1m 2m gb_26<br> 2m 3m gb_4<br> 2m 4m gb_9<br> 4m 5m gb_2<br> 4m 6m gb_20<br> 6m 7m gb_26<br> 7m 8m gb_14<br> 8m 19m gb_9<br> 8m 9m gb_9<br> 19m 17m gb_9<br> 17m 18m gb_2<br> 17m 16m gb_9<br> 16m 9m gb_15<br> 9m 10m gb_15<br> 10m 11m gb_15<br> 11m 14m gb_15<br> 14m
15m gb_15<br> 15m 16m gb_15<br> 11m 12m gb_12<br> 12m 13m gb_17<br> [ angles ]<br>; ai aj ak gromos type<br> 1m 2m 3m ga_29<br> 1m 2m 4m ga_18<br> 3m 2m 4m ga_32<br> 2m 4m 5m ga_31<br> 2m 4m 6m ga_30<br> 5m 4m 6m ga_17<br> 4m 6m 7m ga_12<br> 6m 7m 8m ga_14<br> 7m 8m 19m ga_36<br> 8m 19m 17m ga_6<br> 19m 17m 18m ga_35<br> 19m 17m 16m ga_6<br> 19m 8m 9m ga_6<br> 8m 9m 16m ga_6<br> 9m 16m 17m ga_6<br> 17m 16m 15m ga_38<br> 8m 9m 10m ga_38<br> 16m 9m 10m ga_26<br> 9m 10m 11m ga_26<br> 10m 11m 14m ga_26<br> 11m 14m 15m ga_26<br> 14m 15m 16m ga_26<br> 15m 16m 9m ga_26<br> 10m 11m 12m ga_18<br> 11m 12m 13m ga_11<br> 14m 11m 12m ga_18<br> [ impropers ]<br>; ai aj ak al gromos type<br> 2m 1m 4m 3m gi_1<br> 4m 2m 5m 6m g
i_1<br> 8m 19m 9m 7m gi_1<br> 9m 8m 16m 10m gi_1<br> 11m 14m 12m 10m gi_1<br> 16m 9m 15m 17m gi_1<br> 17m 16m 18m 19m gi_1<br> 8m 9m 16m 17m gi_1<br> 9m 16m 17m 19m gi_1<br> 16m 17m 19m 8m gi_1<br> 17m 19m 8m 9m gi_1<br> 19m 8m 9m 16m gi_1<br> 9m 10m 11m 14m gi_1<br> 10m 11m 14m 15m gi_1<br> 11m 14m 15m 16m gi_1<br> 14m 15m 16m 9m gi_1<br> 15m 16m 9m 10m gi_1<br> 16m 9m 10m 11m gi_1<br> [ dihedrals ]<br>; ai aj ak al gromos type<br> 1m 2m 4m 6m gd_4<br> 7m 6m 4m 2m gd_19<br> 8m 7m 6m 4m gd_17<br> 19m 8m 7m 6m gd_20<br> 10m 11m 12m 13m gd_2<br><br>_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href
="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></pre>
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