<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Justin, thanks a lot. I got the pdb2gmx to work now by changing the .hdb. I hope the simulation will be smooth sailing as well. <br>Thanks,<br>Jerez<br><br>--- On <b>Tue, 2/1/11, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] lactam bridge problems<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Tuesday, February 1, 2011, 11:57 AM<br><br><div class="plainMail"><br><br>Jerez Te wrote:<br>> <br>> I want to create a peptide bond between glu and lys using Gromacs<br>> 4.5.3. One option that I have is to modify the topology file (bonds,<br>> angles, etc.) but I
also want to do a number of these lactam bridges<br>> so it is a pain to make the bonds, delete the atoms in glu and lys<br>> that are not needed and renumber the .itp and .gro files.<br>> <br>> The other option is to add the lactam glu (LCE) and lactam lys (LCK)<br>> as residues to the force field. So far I have added LCE and LCK to<br>> gromos53a6 and opls-aa but i always get the same error: "Atom HZ1<br>> not found in rtp database in residue LCK, it looks a bit like HZ" -<br>> there is no HZ1 in all my files but pdb2gmx seem to be looking for it.<br>> <br>> The naming is consistent (HZ is specified in the .rtp files, in the<br>> pdb file). Here are the modiifcation that I made involving gromos53a6.<br>>
<br>> Following the "Adding a residue to a force field section" in the<br>> gromacs website<br>> 1.)<br>> -------- In aminoacids.rtp (I'm just showing LCK)<br>> [ LCK ]<br>> [ atoms ]<br>> N N -0.31000 0<br>> H H 0.31000 0<br>> CA CH1 0.00000 1<br>> CB CH2 0.00000 1<br>> CG CH2 0.00000 2<br>>
CD CH2 0.00000 2<br>> CE CH2 0.00000 3<br>> NZ N -0.31000 3 ; same atom type as amide N<br>> HZ H 0.31000 3 ; same atom type as amide H<br>> C C 0.450 4<br>> O O -0.450 4<br>> [ bonds ]<br>> N H gb_2<br>> N CA
gb_21<br>> CA CB gb_27<br>> CA C gb_27<br>> CB CG gb_27<br>> CG CD gb_27<br>> CD CE gb_27<br>> CE NZ gb_21 ; same bond as N-CA<br>> NZ HZ gb_2 ; same bond as N-H<br>> C O gb_5<br>> C +N gb_10<br>> [ angles ]<br>> ; ai aj ak gromos type<br>> -C N
H ga_32<br>> -C N CA ga_31<br>> H N CA ga_18<br>> N CA CB ga_13<br>> N CA C ga_13<br>> CB CA C ga_13<br>> CA CB CG ga_15<br>> CB CG CD ga_15<br>> CG CD CE ga_15<br>> CD
CE NJ ga_15<br>> CE NJ HJ ga_31<br>> CA C O ga_30<br>> CA C +N ga_19<br>> O C +N ga_33<br>> [ impropers ]<br>> ; ai aj ak al gromos type<br>> N -C CA H gi_1<br>> CA N C CB gi_2<br>>
C CA +N O gi_1<br>> [ dihedrals ]<br>> ; ai aj ak al gromos type<br>> -CA -C N CA gd_14<br>> -C N CA C gd_39<br>> N CA CB CG gd_34<br>> N CA C +N gd_40<br>> CA CB CG CD gd_34<br>> CB
CG CD CE gd_34<br>> CG CD CE NJ gd_34<br>> CD CE NJ HJ gd_29<br>> <br>> 2.) HBD has been update<br>> LCK 2<br>> 1 1 H N -C CA<br>> 2 4 HZ NZ CE CD<br>> <br>> 3.) no new atom types introduced atomtypes.atp and ffnonbonded.itp<br>> not modified. Note: I did try introducing
new atom types in a<br>> previous attempt (not on this attempt) but I still get the same<br>> error above. <br>> 4.) no new bond types introduced (ffbonded.itp is not modified).<br>> <br>> 5.) In residuetypes.dat (the new residues were declared)<br>> LCK Protein<br>> LCE Protein<br>> <br>> 6.) specbond.dat (the peptide bond was introduced)<br>> LCE CD 1 LCK NZ 1 0.133 LCTM LCTM<br>> <br>> It seems like pdb2gmx is still looking at my new residues as if
they<br>> were lys and glu and that might be the source of the error (In my<br>> original pdb file, LCE and LCK were used so the error does not come<br>> from there and the atom names are also consistent).<br>> Here's a portion of the pdb file that I used:<br>> <br>> ATOM 1759 N LCK B 20 -3.985 -0.668 6.218 1.00<br>> 20.00 N<br>> ATOM 1760 CA LCK B 20 -3.534 -1.515 5.127 1.00<br>> 20.00 C<br>> ATOM 1761 C LCK
B 20 -2.096 -1.976 5.372 1.00<br>> 20.00 C<br>> ATOM 1762 O LCK B 20 -1.823 -3.174 5.413 1.00<br>> 20.00 O<br>> ATOM 1763 HA LCK B 20 -4.173 -2.398 5.113 1.00<br>> 20.00 H<br>> ATOM 1764 CB LCK B 20 -3.662 -0.780 3.790 1.00<br>> 20.00 C<br>>
ATOM 1765 1HB LCK B 20 -4.701 -0.500 3.623 1.00<br>> 20.00 H<br>> ATOM 1766 2HB LCK B 20 -3.084 0.143 3.823 1.00<br>> 20.00 H<br>> ATOM 1767 CG LCK B 20 -3.171 -1.655 2.635 1.00<br>> 20.00 C<br>> ATOM 1768 1HG LCK B 20 -2.125 -1.918 2.792 1.00<br>> 20.00
H<br>> ATOM 1769 2HG LCK B 20 -3.735 -2.588 2.616 1.00<br>> 20.00 H<br>> ATOM 1770 CD LCK B 20 -3.326 -0.932 1.296 1.00<br>> 20.00 C<br>> ATOM 1771 1HD LCK B 20 -3.061 0.119 1.413 1.00<br>> 20.00 H<br>> ATOM 1772 2HD LCK B 20 -2.635 -1.356 0.567 1.00<br>> 20.00
H<br>> ATOM 1773 CE LCK B 20 -4.760 -1.047 0.774 1.00<br>> 20.00 C<br>> ATOM 1774 1HE LCK B 20 -4.973 -2.081 0.503 1.00<br>> 20.00 H<br>> ATOM 1775 2HE LCK B 20 -5.463 -0.771 1.560 1.00<br>> 20.00 H<br>> ATOM 1776 NZ LCK B 20 -4.955 -0.170 -0.403 1.00<br>>
20.00 N<br>> ATOM 1777 HZ LCK B 20 -5.909 -0.258 -0.736 1.00<br>> 20.00 H<br>> ATOM 1778 HN LCK B 20 -3.255 -0.255 6.762 1.00<br>> 20.00 H<br>> <br>> Any suggestion as to how to solve this error? <br><br>I will assume that you're using -ignh with pdb2gmx? Otherwise, you'd be getting a fatal error about about HN not being found in the .rtp entry. You've constructed your .hdb file such that pdb2gmx is going to try to add 2 HZ atoms (thus HZ1 and HZ2), and hence the fatal error.<br><br>-Justin<br><br>--
========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">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>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use
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