<div>Not really, I mentioned that based on Sorin's ffamber page:</div><div><br></div><div>a)<span class="Apple-tab-span" style="white-space:pre"> </span></div><div>Non-terminal amino and nucleic acid residues follow standard AMBER naming conventions. To avoid confusion between GROMACS and AMBER conventions, we have omitted the redundant HIS residue, leaving HID, HIE, HIP, and terminal versions of these topologies. Additionally, due to the automated changing of certain residue names by pdb2gmx, the LYS and CYS residues have been renamed LYP (Lysine plus) and CYN (Cysteine neutral, compared to AMBER residue CYM = Cysteine minus).</div>
<div>(b)<span class="Apple-tab-span" style="white-space:pre"> </span></div><div>C- and N-terminal amino acids include a C or N prefix respectively, so C-terminal ALA is CALA and N-ternimal PHE is NPHE. As with non-terminal versions, the LYS and CYS terminal residues are listed as NLYP,CLYP and NCYN,CCYN.</div>
<div><br></div><div>And I did mistake, it's not CYP, but CYN.</div><div><br></div><div>So I don't know if you are fully following Sorin's recommendations.</div><div><br></div><br><div class="gmail_quote">On 25 August 2010 14:36, 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>
You can find the residue name to rtp translation table in:<br>share/top/amber99.ff/aminoacids.r2b<br><br>I don't have a list with Amber names and funtions for the amino acids.<br>Currently for Amber in Gromacs we have CYS (standard, neutral, protonated)<br>
and CYX (disulfide bond).<br>Does Amber use CYP instead of CYS?<div class="im"><br><br>Berk<br><br><hr>From: <a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a><br></div>Date: Wed, 25 Aug 2010 14:17:58 +0100<div>
<div></div><div class="h5"><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>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>On 25 August 2010 13:59, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote style="border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div>
Hi,<br><br>I now turned on the automatic HIE, and analogous, terminal renaming on by default.<div><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><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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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<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>