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Hi,<br><br>I just ran pdb2gmx (4.0.5 and git master) with AMBER on a test di-peptide.<br>But for me all H's in the NH3 terminus always end up in different charge-groups.<br>No matter if I use v-sites or not and if use -ignh or not.<br>So I don't understand how you managed to get the H's in the same charge group.<br><br>Berk<br><br>> Date: Wed, 30 Sep 2009 18:14:06 +0200<br>> From: jochen@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes<br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> ><br>> > Are you 100% sure you have no other charge groups in your system<br>> > that consist of only virtual sites, but at least with 2 virtual sites?<br>> Ah, you're right. One of the CG which caused the crash is the following, <br>> with 2 H's in one CG:<br>> <br>> 1 amber99_39 1 NPRO N 1 -0.202 16.026 ; <br>> qtot -0.202<br>> 2 amber99_17 1 NPRO H1 2 (!) 0.312 <br>> 0 ; qtot 0.11<br>> 3 amber99_17 1 NPRO H2 2 (!) 0.312 0 <br>> ; qtot 0.422<br>> 4 amber99_11 1 NPRO CD 3 -0.012 14.026 ; <br>> qtot 0.41<br>> <br>> Note however, that the CG which also caused crashes was different, with <br>> 2 vsites and 1 heavy atom in the same group, plus a separate CG with 3 <br>> hydrogens. According to the lincs warning and 1-4 distance error, the <br>> hydrogens seemed to be involved. Typically the warning/error mentioned <br>> the hydrogen to have moved/rotated too much:<br>> <br>> 1 MNH3 1 NASN MN1 1 0 8.517 ; <br>> qtot 0<br>> 2 MNH3 1 NASN MN2 1 0 8.517 ; <br>> qtot 0<br>> 3 amber99_39 1 NASN N 1 0.1801 0 ; <br>> qtot 0.1801<br>> 4 amber99_17 1 NASN H1 2 0.1921 0 ; <br>> qtot 0.3722<br>> 5 amber99_17 1 NASN H2 2 0.1921 0 ; <br>> qtot 0.5643<br>> 6 amber99_17 1 NASN H3 2 0.1921 0 ; <br>> qtot 0.7564<br>> 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; <br>> qtot 0.7932<br>> <br>> ><br>> > I just fixed a bug with this situation for 4.0.6 and 4.1.<br>> > You can try the git master or 4.0 release branch.<br>> I will get the lates gmx with your bugfix and write back if the crashes <br>> still appear.<br>> <br>> ><br>> > I don't understand why only your terminal NH3 becomes a single charge <br>> > group,<br>> > unless the hydrogens were generated with the .hdb file,<br>> > while they were present for all other NH3 groups.<br>> I don't understand that either. The result is the same no matter if I <br>> use -ignh, or if the hydrogens are present in the input gro file or not. <br>> For examle, using<br>> <br>> pdb2gmx -f asn[-h].gro -ff amber99sb [-ignh]<br>> <br>> with asn-h.gro or asn.gro are just the ASN at the N-terminus (with or <br>> without hydrogens), e.g. asn-h.gro:<br>> <br>> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon<br>> 8<br>> 97NASN N 1423 0.062 -1.317 1.235<br>> 97NASN CA 1427 0.109 -1.209 1.154<br>> 97NASN CB 1429 0.233 -1.249 1.073<br>> 97NASN CG 1432 0.213 -1.368 0.981<br>> 97NASN OD1 1433 0.263 -1.478 1.005<br>> 97NASN ND2 1434 0.143 -1.345 0.867<br>> 97NASN C 1437 0.003 -1.148 1.068<br>> 97NASN O 1438 0.033 -1.090 0.964<br>> 0.00000 0.00000 0.00000<br>> <br>> The written topology is:<br>> <br>> [ atoms ]<br>> ; nr type resnr residue atom cgnr charge mass <br>> typeB chargeB massB<br>> 1 amber99_39 1 NASN N 1 0.1801 14.01 ; <br>> qtot 0.1801<br>> 2 amber99_17 1 NASN H1 2 0.1921 1.008 ; <br>> qtot 0.3722<br>> 3 amber99_17 1 NASN H2 2 0.1921 1.008 ; <br>> qtot 0.5643<br>> 4 amber99_17 1 NASN H3 2 0.1921 1.008 ; <br>> qtot 0.7564<br>> 5 amber99_11 1 NASN CA 3 0.0368 12.01 ; <br>> qtot 0.7932<br>> 6 amber99_28 1 NASN HA 4 0.1231 1.008 ; <br>> qtot 0.9163<br>> ...<br>> <br>> Weird. The same thing happens by the way with a proline N-terminus, no <br>> matter if hydrogens are present before pdb2gmx or not.<br>> <br>> So thanks a lot for the help,<br>> <br>> Jochen<br>> <br>> ><br>> > Berk<br>> ><br>> > > Date: Wed, 30 Sep 2009 16:45:39 +0200<br>> > > From: jochen@xray.bmc.uu.se<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, <br>> > and crashes<br>> > ><br>> > > Hey Berk,<br>> > ><br>> > > I just found that the simulation with a separate CG on each atom also<br>> > > crashed, but much later (after 11ns), that why I just noticed that. I<br>> > > have repeated the simulations now to make really sure that the crashes<br>> > > are reproducible.<br>> > ><br>> > > Jochen<br>> > ><br>> > ><br>> > > Jochen Hub wrote:<br>> > > ><br>> > > > I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try <br>> > someting<br>> > > > else?<br>> > > ><br>> > > > Jochen<br>> > > ><br>> > > ><br>> > > > Berk Hess wrote:<br>> > > >> Hi,<br>> > > >><br>> > > >> One question:<br>> > > >> Are these crashes single processor, with domain decomposition, or <br>> > both?<br>> > > >><br>> > > >> Berk<br>> > > >><br>> > > >> > Date: Wed, 30 Sep 2009 15:35:42 +0200<br>> > > >> > From: jochen@xray.bmc.uu.se<br>> > > >> > To: gmx-users@gromacs.org<br>> > > >> > Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus,<br>> > > >> and crashes<br>> > > >> ><br>> > > >> > Hi,<br>> > > >> ><br>> > > >> > I have been trying to use vsites with AMBER99SB, but the simulation<br>> > > >> > frequently cashes after a few hundred ps with the suspects (lincs<br>> > > >> > warnings, 1-4 distance error). I could pinpoint the problem to<br>> > > >> erroneous<br>> > > >> > charge group assignments generated by pdb2gmx at the NH3 group <br>> > at the<br>> > > >> > N-terminus. The following charge group assignments caused the <br>> > error:<br>> > > >> ><br>> > > >> > ; nr type resnr residue atom cgnr charge mass<br>> > > >> > 1 MNH3 1 NASN MN1 1 0 8.517 ;<br>> > > >> > qtot 0<br>> > > >> > 2 MNH3 1 NASN MN2 1 0 8.517 ;<br>> > > >> > qtot 0<br>> > > >> > 3 amber99_39 1 NASN N 1 0.1801 0 ;<br>> > > >> > qtot 0.1801<br>> > > >> > 4 amber99_17 1 NASN H1 2 0.1921 0 ;<br>> > > >> > qtot 0.3722<br>> > > >> > 5 amber99_17 1 NASN H2 2 0.1921 0 ;<br>> > > >> > qtot 0.5643<br>> > > >> > 6 amber99_17 1 NASN H3 2 0.1921 0 ;<br>> > > >> > qtot 0.7564<br>> > > >> > 7 amber99_11 1 NASN CA 3 0.0368 13.018 ;<br>> > > >> > qtot 0.7932<br>> > > >> > ...<br>> > > >> ><br>> > > >> > The NH3 groups in the lysines were fine and did not cause any<br>> > > >> error. The<br>> > > >> > only difference compared to the N-terminus is that each of the <br>> > three H<br>> > > >> > in the NH3 has its own charge group, but the vsites and the N are<br>> > > >> still<br>> > > >> > in the same CG:<br>> > > >> ><br>> > > >> > 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ;<br>> > > >> > qtot 0.9937<br>> > > >> > 31 amber99_28 2 LYP HE1 30 0.1135 0 ;<br>> > > >> > qtot 1.107<br>> > > >> > 32 amber99_28 2 LYP HE2 31 0.1135 0 ;<br>> > > >> > qtot 1.221<br>> > > >> > 33 MNH3 2 LYP MNZ1 32 0 8.517 ;<br>> > > >> > qtot 1.221<br>> > > >> > 34 MNH3 2 LYP MNZ2 32 0 8.517 ;<br>> > > >> > qtot 1.221<br>> > > >> > 35 amber99_39 2 LYP NZ 32 -0.3854 0 ;<br>> > > >> > qtot 0.8353<br>> > > >> > 36 amber99_17 2 LYP HZ1 33 0.34 0 ;<br>> > > >> > qtot 1.175<br>> > > >> > 37 amber99_17 2 LYP HZ2 34 0.34 0 ;<br>> > > >> > qtot 1.515<br>> > > >> > 38 amber99_17 2 LYP HZ3 35 0.34 0 ;<br>> > > >> > qtot 1.855<br>> > > >> ><br>> > > >> > Alternatively, I have also tried to give every single atom <br>> > (including<br>> > > >> > the vsites MN??) a separate charge group, which also worked fine.<br>> > > >> ><br>> > > >> > 1)<br>> > > >> > So, is there any reason why the dummies should be in the same <br>> > CG as<br>> > > >> the<br>> > > >> > nitrogen? Or should it be fine just to assign a separate CG to<br>> > > >> every atom?<br>> > > >> ><br>> > > >> > 2)<br>> > > >> > Is a bug report appreciated on that issue?<br>> > > >> ><br>> > > >> > Best,<br>> > > >> ><br>> > > >> > Jochen<br>> > > >> ><br>> > > >> ><br>> > > >> > --<br>> > > >> > ---------------------------------------------------<br>> > > >> > Dr. Jochen Hub<br>> > > >> > Molecular Biophysics group<br>> > > >> > Dept. of Cell & Molecular Biology<br>> > > >> > Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>> > > >> > Phone: +46-18-4714451 Fax: +46-18-511755<br>> > > >> > ---------------------------------------------------<br>> > > >> ><br>> > > >> > _______________________________________________<br>> > > >> > gmx-users mailing list gmx-users@gromacs.org<br>> > > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > >> > Please search the archive at http://www.gromacs.org/search before<br>> > > >> posting!<br>> > > >> > Please don't post (un)subscribe requests to the list. Use the<br>> > > >> > www interface or send it to gmx-users-request@gromacs.org.<br>> > > >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > >><br>> > > >> <br>> > ------------------------------------------------------------------------<br>> > > >> See all the ways you can stay connected to friends and family<br>> > > >> <http://www.microsoft.com/windows/windowslive/default.aspx><br>> > > >> <br>> > ------------------------------------------------------------------------<br>> > > >><br>> > > >> _______________________________________________<br>> > > >> gmx-users mailing list gmx-users@gromacs.org<br>> > > >> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > >> Please search the archive at http://www.gromacs.org/search before<br>> > > >> posting!<br>> > > >> Please don't post (un)subscribe requests to the list. Use the www<br>> > > >> interface or send it to gmx-users-request@gromacs.org.<br>> > > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > ><br>> > > ><br>> > ><br>> > ><br>> > > --<br>> > > ---------------------------------------------------<br>> > > Dr. Jochen Hub<br>> > > Molecular Biophysics group<br>> > > Dept. of Cell & Molecular Biology<br>> > > Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>> > > Phone: +46-18-4714451 Fax: +46-18-511755<br>> > > ---------------------------------------------------<br>> > ><br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> > ------------------------------------------------------------------------<br>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > ------------------------------------------------------------------------<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -- <br>> ---------------------------------------------------<br>> Dr. Jochen Hub<br>> Molecular Biophysics group<br>> Dept. of Cell & Molecular Biology<br>> Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>> Phone: +46-18-4714451 Fax: +46-18-511755<br>> ---------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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