Just one more question. How are you handling CYS? In amber it could be CYP, CYN etc.
Thanks a lot, Alan On 25 August 2010 13:59, Berk Hess <[email protected]> wrote: > Hi, > > I now turned on the automatic HIE, and analogous, terminal renaming on by > default. > > > Berk > > ------------------------------ > From: [email protected] > To: [email protected] > Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now > Date: Wed, 25 Aug 2010 14:34:30 +0200 > > > Hi, > > I fixed all the terminal residue issues. > > The automatic HIE terminal translation is still swtiched by the env.var. > I'm still thinking if there could be issues when we turn that always on. > > Berk > > ------------------------------ > From: [email protected] > Date: Tue, 24 Aug 2010 22:55:57 +0100 > Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now > To: [email protected] > > Dear Berk, > > I understand your point and this can be very confusing. > > I am aware that I could use HIS and then pdb2gmx ... -his (option 1), but > this is not working either with rev. d6298. Error: > > [snip] > Which HISTIDINE type do you want for residue 3 > 0. H on ND1 only (HID) > 1. H on NE2 only (HIE) > 2. H on ND1 and NE2 (HIP) > 3. Coupled to Heme (HIS1) > > Type a number:1 > Identified residue HIS1 as a starting terminus. > Identified residue HIS3 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Special Atom Distance matrix: > HIS1 HIS2 > NE214 NE231 > HIS2 NE231 0.854 > HIS3 NE248 0.751 0.847 > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298 > Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line: > 552 > > Fatal error: > Residue 'HISE' not found in residue topology database > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > The pdb I am using is hhh.pdb > ATOM 1 N HIS 1 3.389 1.609 -0.001 1.00 0.00 > N > ATOM 2 H1 HIS 1 4.107 0.893 -0.048 1.00 0.00 > H > ATOM 3 H2 HIS 1 2.795 1.549 -0.816 1.00 0.00 > H > ATOM 4 H3 HIS 1 2.844 1.452 0.836 1.00 0.00 > H > ATOM 5 CA HIS 1 4.058 2.928 0.075 1.00 0.00 > C > ATOM 6 HA HIS 1 3.894 3.469 -0.857 1.00 0.00 > H > ATOM 7 CB HIS 1 3.469 3.750 1.230 1.00 0.00 > C > ATOM 8 HB2 HIS 1 2.384 3.783 1.126 1.00 0.00 > H > ATOM 9 HB3 HIS 1 3.695 3.231 2.164 1.00 0.00 > H > ATOM 10 CG HIS 1 3.956 5.172 1.373 1.00 0.00 > C > ATOM 11 ND1 HIS 1 4.013 5.834 2.591 1.00 0.00 > N > ATOM 12 CE1 HIS 1 4.604 7.011 2.356 1.00 0.00 > C > ATOM 13 HE1 HIS 1 4.832 7.752 3.115 1.00 0.00 > H > ATOM 14 NE2 HIS 1 4.919 7.122 1.056 1.00 0.00 > N > ATOM 15 HE2 HIS 1 5.505 7.845 0.657 1.00 0.00 > H > ATOM 16 CD2 HIS 1 4.479 5.987 0.403 1.00 0.00 > C > ATOM 17 HD2 HIS 1 4.620 5.781 -0.645 1.00 0.00 > H > ATOM 18 C HIS 1 5.564 2.693 0.196 1.00 0.00 > C > ATOM 19 O HIS 1 5.947 1.551 0.422 1.00 0.00 > O > ATOM 20 N HIS 2 6.376 3.718 -0.053 1.00 0.00 > N > ATOM 21 H HIS 2 5.980 4.646 -0.135 1.00 0.00 > H > ATOM 22 CA HIS 2 7.843 3.744 -0.109 1.00 0.00 > C > ATOM 23 HA HIS 2 8.260 3.319 0.806 1.00 0.00 > H > ATOM 24 CB HIS 2 8.319 2.925 -1.327 1.00 0.00 > C > ATOM 25 HB2 HIS 2 7.855 1.940 -1.312 1.00 0.00 > H > ATOM 26 HB3 HIS 2 7.985 3.435 -2.233 1.00 0.00 > H > ATOM 27 CG HIS 2 9.807 2.703 -1.450 1.00 0.00 > C > ATOM 28 ND1 HIS 2 10.461 2.463 -2.655 1.00 0.00 > N > ATOM 29 CE1 HIS 2 11.770 2.542 -2.382 1.00 0.00 > C > ATOM 30 HE1 HIS 2 12.557 2.484 -3.124 1.00 0.00 > H > ATOM 31 NE2 HIS 2 11.969 2.794 -1.078 1.00 0.00 > N > ATOM 32 HE2 HIS 2 12.817 3.173 -0.672 1.00 0.00 > H > ATOM 33 CD2 HIS 2 10.740 2.839 -0.459 1.00 0.00 > C > ATOM 34 HD2 HIS 2 10.579 3.098 0.574 1.00 0.00 > H > ATOM 35 C HIS 2 8.279 5.228 -0.214 1.00 0.00 > C > ATOM 36 O HIS 2 7.440 6.079 -0.525 1.00 0.00 > O > ATOM 37 N HIS 3 9.547 5.520 0.075 1.00 0.00 > N > ATOM 38 H HIS 3 10.192 4.759 0.245 1.00 0.00 > H > ATOM 39 CA HIS 3 10.254 6.807 0.049 1.00 0.00 > C > ATOM 40 HA HIS 3 10.021 7.358 -0.860 1.00 0.00 > H > ATOM 41 CB HIS 3 9.841 7.621 1.297 1.00 0.00 > C > ATOM 42 HB2 HIS 3 8.754 7.687 1.320 1.00 0.00 > H > ATOM 43 HB3 HIS 3 10.158 7.074 2.185 1.00 0.00 > H > ATOM 44 CG HIS 3 10.359 9.037 1.429 1.00 0.00 > C > ATOM 45 ND1 HIS 3 10.137 9.848 2.546 1.00 0.00 > N > ATOM 46 CE1 HIS 3 10.788 10.994 2.308 1.00 0.00 > C > ATOM 47 HE1 HIS 3 10.849 11.818 3.006 1.00 0.00 > H > ATOM 48 NE2 HIS 3 11.375 10.962 1.100 1.00 0.00 > N > ATOM 49 HE2 HIS 3 11.977 11.674 0.715 1.00 0.00 > H > ATOM 50 CD2 HIS 3 11.100 9.742 0.525 1.00 0.00 > C > ATOM 51 HD2 HIS 3 11.456 9.376 -0.428 1.00 0.00 > H > ATOM 52 C HIS 3 11.761 6.487 0.002 1.00 0.00 > C > ATOM 53 O HIS 3 12.128 5.407 0.518 1.00 0.00 > O > ATOM 54 OXT HIS 3 12.494 7.275 -0.632 1.00 0.00 > O > > Now, using HIE (HHH.pdb, like hhh.pdb but HIE for res instead of HIS) with > export GMX_FFRTP_TER_RENAME=1 and then > > pdb2gmx -f HHH.pdb -o HHH.pdb -p agHHH.top -ff amber99sb -water none > > works. > > echo 1 1 1 | pdb2gmx -f hhh.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb > -water none -his > > will work as well as long as I replace HB3 by HB1 or use -ignh, but > attention, without GMX_FFRTP_TER_RENAME, it doesn't work. > > I hope it can help. > > Cheers, > > Alan > > On 24 August 2010 20:14, Berk Hess <[email protected]> wrote: > > Hi, > > I asked the authors of the gmx amber ports what the desired behavior would > be. > For the time being I committed the fix, but it only gets activated when you > have > the env.var. GMX_FFRTP_TER_RENAME set. > > Berk > > ------------------------------ > From: [email protected] > > To: [email protected] > Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now > Date: Tue, 24 Aug 2010 20:48:05 +0200 > > > Hi, > > I have made a fix, but am now wondering if we actually want to fix this. > HIE is not a standard pdb residue name. > A file with HIS-HIS-HIS would work. > HIE is an Amber name and in that case one might say that you should use: > NHIE-HIE-CHIE. > But I don't know what the Amber program would support for input. > > PS NHIE is now listed incorrectly as NHISE in residuetypes.dat, > so NHIE-HIE-CHIE won't work. I'll at least commit a fix for that. > > Berk > > ------------------------------ > From: [email protected] > Date: Tue, 24 Aug 2010 18:06:45 +0100 > Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now > To: [email protected] > > I am using gmx 4.5 d748b. > > Thanks Berk, it seems to be working ... for DNA. > > But this one is broken (and it was working before): HHH is tripetide > Hie-Hie-Hie. > > pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none > > [snip] > Identified residue HIE1 as a starting terminus. > Identified residue HIE3 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b > Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: > 916 > > Fatal error: > There is a dangling bond at at least one of the terminal ends and the force > field does not provide terminal entries or files. Edit a .n.tdb and/or > .c.tdb file. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Alan > > On 24 August 2010 15:30, Berk Hess <[email protected]> wrote: > > Hi, > > I fixed it. > Thanks for the fast test and the complete instructions, > > Berk > > ------------------------------ > From: [email protected] > Date: Tue, 24 Aug 2010 15:22:34 +0100 > To: [email protected] > Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now > > > Hi there, in special Berk. > > So pdb2gmx may be working with HIS and variants for oplsaa but now, > something that was working before is failing: > > wget -c "http://www.pdbe.org/download/1BNA"; -O 1BNA.pdb > grep 'ATOM ' 1BNA.pdb >| DNA.pdb > > cat << EOF >| SPE.mdp > define = -DFLEXIBLE > integrator = md > nsteps = 0 > dt = 0.001 > constraints = none > emtol = 10.0 > emstep = 0.01 > nstcomm = 1 > ns_type = simple > nstlist = 0 > rlist = 0 > rcoulomb = 0 > rvdw = 0 > Tcoupl = no > Pcoupl = no > gen_vel = no > nstxout = 1 > pbc = no > nstlog = 1 > nstenergy = 1 > nstvout = 1 > nstfout = 1 > nstxtcout = 1 > comm_mode = ANGULAR > continuation = yes > EOF > > pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p > DnaAmberSBGMX45 > [snip] > 8 out of 8 lines of specbond.dat converted successfully > [1] 42209 segmentation fault pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb > -ff amber99sb -water none -p > > with 5e347 it worded fine, i.e, it opens files > > Opening force field file > /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn > Opening force field file > /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn > Opening force field file > /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn > > and proceed. > > Alan > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><< > > -- 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 the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><< > > -- 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 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 the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><< > > -- 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 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 the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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