Just one more question. How are you handling CYS? In amber it could be CYP, CYN etc.<br><br><div>Thanks a lot,</div><div><br></div><div>Alan</div><div><br><div class="gmail_quote">On 25 August 2010 13:59, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
Hi,<br><br>I now turned on the automatic HIE, and analogous, terminal renaming on by default.<div class="im"><br><br>Berk<br><br><hr>From: <a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now<br></div>Date: Wed, 25 Aug 2010 14:34:30 +0200<div><div></div><div class="h5"><br><br>
Hi,<br><br>I fixed all the terminal residue issues.<br><br>The automatic HIE terminal translation is still swtiched by the env.var.<br>I'm still thinking if there could be issues when we turn that always on.<br><br>Berk<br>
<br><hr>From: <a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a><br>Date: Tue, 24 Aug 2010 22:55:57 +0100<br>Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now<br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<br>Dear Berk,<div><br></div><div>I understand your point and this can be very confusing.</div><div><br></div><div>I am aware that I could use HIS and then pdb2gmx ... -his (option 1), but this is not working either with rev. d6298. Error:</div>
<div><br></div><div>[snip]</div><div><div>Which HISTIDINE type do you want for residue 3</div><div>0. H on ND1 only (HID)</div><div>1. H on NE2 only (HIE)</div><div>2. H on ND1 and NE2 (HIP)</div><div>3. Coupled to Heme (HIS1)</div>
<div><br></div><div>Type a number:1</div><div>Identified residue HIS1 as a starting terminus.</div><div>Identified residue HIS3 as a ending terminus.</div><div>8 out of 8 lines of specbond.dat converted successfully</div>
<div>Special Atom Distance matrix:</div><div> HIS1 HIS2</div><div> NE214 NE231</div><div> HIS2 NE231 0.854</div><div> HIS3 NE248 0.751 0.847</div><div><br></div><div>
-------------------------------------------------------</div><div>Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298</div><div>Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line: 552</div><div><br>
</div><div>Fatal error:</div><div>Residue 'HISE' not found in residue topology database</div><div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div>
<div><br></div><div>The pdb I am using is hhh.pdb </div><div><div>ATOM 1 N HIS 1 3.389 1.609 -0.001 1.00 0.00 N</div><div>ATOM 2 H1 HIS 1 4.107 0.893 -0.048 1.00 0.00 H</div>
<div>ATOM 3 H2 HIS 1 2.795 1.549 -0.816 1.00 0.00 H</div><div>ATOM 4 H3 HIS 1 2.844 1.452 0.836 1.00 0.00 H</div><div>ATOM 5 CA HIS 1 4.058 2.928 0.075 1.00 0.00 C</div>
<div>ATOM 6 HA HIS 1 3.894 3.469 -0.857 1.00 0.00 H</div><div>ATOM 7 CB HIS 1 3.469 3.750 1.230 1.00 0.00 C</div><div>ATOM 8 HB2 HIS 1 2.384 3.783 1.126 1.00 0.00 H</div>
<div>ATOM 9 HB3 HIS 1 3.695 3.231 2.164 1.00 0.00 H</div><div>ATOM 10 CG HIS 1 3.956 5.172 1.373 1.00 0.00 C</div><div>ATOM 11 ND1 HIS 1 4.013 5.834 2.591 1.00 0.00 N</div>
<div>ATOM 12 CE1 HIS 1 4.604 7.011 2.356 1.00 0.00 C</div><div>ATOM 13 HE1 HIS 1 4.832 7.752 3.115 1.00 0.00 H</div><div>ATOM 14 NE2 HIS 1 4.919 7.122 1.056 1.00 0.00 N</div>
<div>ATOM 15 HE2 HIS 1 5.505 7.845 0.657 1.00 0.00 H</div><div>ATOM 16 CD2 HIS 1 4.479 5.987 0.403 1.00 0.00 C</div><div>ATOM 17 HD2 HIS 1 4.620 5.781 -0.645 1.00 0.00 H</div>
<div>ATOM 18 C HIS 1 5.564 2.693 0.196 1.00 0.00 C</div><div>ATOM 19 O HIS 1 5.947 1.551 0.422 1.00 0.00 O</div><div>ATOM 20 N HIS 2 6.376 3.718 -0.053 1.00 0.00 N</div>
<div>ATOM 21 H HIS 2 5.980 4.646 -0.135 1.00 0.00 H</div><div>ATOM 22 CA HIS 2 7.843 3.744 -0.109 1.00 0.00 C</div><div>ATOM 23 HA HIS 2 8.260 3.319 0.806 1.00 0.00 H</div>
<div>ATOM 24 CB HIS 2 8.319 2.925 -1.327 1.00 0.00 C</div><div>ATOM 25 HB2 HIS 2 7.855 1.940 -1.312 1.00 0.00 H</div><div>ATOM 26 HB3 HIS 2 7.985 3.435 -2.233 1.00 0.00 H</div>
<div>ATOM 27 CG HIS 2 9.807 2.703 -1.450 1.00 0.00 C</div><div>ATOM 28 ND1 HIS 2 10.461 2.463 -2.655 1.00 0.00 N</div><div>ATOM 29 CE1 HIS 2 11.770 2.542 -2.382 1.00 0.00 C</div>
<div>ATOM 30 HE1 HIS 2 12.557 2.484 -3.124 1.00 0.00 H</div><div>ATOM 31 NE2 HIS 2 11.969 2.794 -1.078 1.00 0.00 N</div><div>ATOM 32 HE2 HIS 2 12.817 3.173 -0.672 1.00 0.00 H</div>
<div>ATOM 33 CD2 HIS 2 10.740 2.839 -0.459 1.00 0.00 C</div><div>ATOM 34 HD2 HIS 2 10.579 3.098 0.574 1.00 0.00 H</div><div>ATOM 35 C HIS 2 8.279 5.228 -0.214 1.00 0.00 C</div>
<div>ATOM 36 O HIS 2 7.440 6.079 -0.525 1.00 0.00 O</div><div>ATOM 37 N HIS 3 9.547 5.520 0.075 1.00 0.00 N</div><div>ATOM 38 H HIS 3 10.192 4.759 0.245 1.00 0.00 H</div>
<div>ATOM 39 CA HIS 3 10.254 6.807 0.049 1.00 0.00 C</div><div>ATOM 40 HA HIS 3 10.021 7.358 -0.860 1.00 0.00 H</div><div>ATOM 41 CB HIS 3 9.841 7.621 1.297 1.00 0.00 C</div>
<div>ATOM 42 HB2 HIS 3 8.754 7.687 1.320 1.00 0.00 H</div><div>ATOM 43 HB3 HIS 3 10.158 7.074 2.185 1.00 0.00 H</div><div>ATOM 44 CG HIS 3 10.359 9.037 1.429 1.00 0.00 C</div>
<div>ATOM 45 ND1 HIS 3 10.137 9.848 2.546 1.00 0.00 N</div><div>ATOM 46 CE1 HIS 3 10.788 10.994 2.308 1.00 0.00 C</div><div>ATOM 47 HE1 HIS 3 10.849 11.818 3.006 1.00 0.00 H</div>
<div>ATOM 48 NE2 HIS 3 11.375 10.962 1.100 1.00 0.00 N</div><div>ATOM 49 HE2 HIS 3 11.977 11.674 0.715 1.00 0.00 H</div><div>ATOM 50 CD2 HIS 3 11.100 9.742 0.525 1.00 0.00 C</div>
<div>ATOM 51 HD2 HIS 3 11.456 9.376 -0.428 1.00 0.00 H</div><div>ATOM 52 C HIS 3 11.761 6.487 0.002 1.00 0.00 C</div><div>ATOM 53 O HIS 3 12.128 5.407 0.518 1.00 0.00 O</div>
<div>ATOM 54 OXT HIS 3 12.494 7.275 -0.632 1.00 0.00 O</div></div><div><br></div><div>Now, using HIE (HHH.pdb, like hhh.pdb but HIE for res instead of HIS) with export <span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse">GMX_FFRTP_TER_RENAME=1 and then</span></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">pdb2gmx -f HHH.pdb -o HHH.pdb -p agHHH.top -ff amber99sb -water none</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">works.</span></font></div>
<div><br></div><div>echo 1 1 1 | pdb2gmx -f hhh.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none -his</div><div><br></div><div>will work as well as long as I replace HB3 by HB1 or use -ignh, but attention, without <span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse">GMX_FFRTP_TER_RENAME, it doesn't work.</span></div>
<div><br></div><div>I hope it can help.</div><div><br></div><div>Cheers,</div><div><br></div><div>Alan</div><br><div>On 24 August 2010 20:14, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote style="padding-left:1ex">
<div>
Hi,<br><br>I asked the authors of the gmx amber ports what the desired behavior would be.<br>For the time being I committed the fix, but it only gets activated when you have<br>the env.var. GMX_FFRTP_TER_RENAME set.<br><br>
Berk<br><br><hr>From: <a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a><div><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now<br>
Date: Tue, 24 Aug 2010 20:48:05 +0200<div><div></div><div><br><br>
Hi,<br><br>I have made a fix, but am now wondering if we actually want to fix this.<br>HIE is not a standard pdb residue name.<br>A file with HIS-HIS-HIS would work.<br>HIE is an Amber name and in that case one might say that you should use:<br>
NHIE-HIE-CHIE.<br>But I don't know what the Amber program would support for input.<br><br>PS NHIE is now listed incorrectly as NHISE in residuetypes.dat,<br>so NHIE-HIE-CHIE won't work. I'll at least commit a fix for that.<br>
<br>Berk<br><br><hr>From: <a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a><br>Date: Tue, 24 Aug 2010 18:06:45 +0100<br>Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><br><div>I am using gmx 4.5 d748b.</div><div><br></div>Thanks Berk, it seems to be working ... for DNA.<div><br></div><div>But this one is broken (and it was working before): HHH is tripetide Hie-Hie-Hie.</div>
<div><br></div><div>
pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none</div><div><br></div><div>[snip]</div><div><div>Identified residue HIE1 as a starting terminus.</div><div>Identified residue HIE3 as a ending terminus.</div>
<div>8 out of 8 lines of specbond.dat converted successfully</div><div><br></div><div>-------------------------------------------------------</div><div>Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b</div><div>Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: 916</div>
<div><br></div><div>Fatal error:</div><div>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.</div><div>For more information and tips for troubleshooting, please check the GROMACS</div>
<div>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div><div><br></div><div>Alan</div><div><br></div><div>On 24 August 2010 15:30, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote style="padding-left:1ex">
<div>
Hi,<br><br>I fixed it.<br>Thanks for the fast test and the complete instructions,<br><br>Berk<br><br><hr>From: <a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a><br>Date: Tue, 24 Aug 2010 15:22:34 +0100<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now<div><div></div><div><br><br>Hi there, in special Berk.<div>
<br></div><div>So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing:</div><div><br></div><div><div>wget -c "<a href="http://www.pdbe.org/download/1BNA" target="_blank">http://www.pdbe.org/download/1BNA</a>" -O 1BNA.pdb</div>
<div>grep 'ATOM ' 1BNA.pdb >| DNA.pdb</div><div><br></div><div><div>cat << EOF >| SPE.mdp</div><div>define = -DFLEXIBLE</div><div>integrator = md</div><div>nsteps = 0</div>
<div>dt = 0.001</div><div>constraints = none</div><div>emtol = 10.0</div><div>emstep = 0.01</div><div>nstcomm = 1</div><div>ns_type = simple</div>
<div>nstlist = 0</div><div>rlist = 0</div><div>rcoulomb = 0</div><div>rvdw = 0</div><div>Tcoupl = no</div><div>Pcoupl = no</div>
<div>gen_vel = no</div><div>nstxout = 1</div><div>pbc = no</div><div>nstlog = 1</div><div>nstenergy = 1</div><div>nstvout = 1</div><div>nstfout = 1</div><div>nstxtcout = 1</div>
<div>comm_mode = ANGULAR</div><div>continuation = yes</div><div>EOF</div></div><div><br></div><div><div>pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45</div><div>[snip]</div></div><div>
<div>8 out of 8 lines of specbond.dat converted successfully</div><div>[1] 42209 segmentation fault pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p </div><div><br></div></div>with 5e347 it worded fine, i.e, it opens files</div>
<div><br></div><div><div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn</div><div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn</div>
<div>Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn</div></div><div><br></div><div>and proceed.</div><div><br></div><div>Alan<br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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