<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Everything beyond dssp 2.0 uses a new syntax, which is not (yet) supported in gromacs. The new way of invoking dssp is described on the dssp webpage. Although undocumented, version 2.0 still accepts the old syntax, but NOT the -na flag, which is set by do_dssp unless you ask for syrface area calculations. Try to either install dssp 1.X or add e.g. the -a flag when executing do_dssp. The latter worked to my surprise.</div><div><br></div><div>There is a fix for this issue up for review that will (hopefully) go into gromacs 4.6. If you can't wait for that, it's pretty straightforward to modify how dssp is invoked in src/tools/do_dssp.c.</div><div><br></div><div>Erik</div><br><div><div>30 mar 2012 kl. 16.38 skrev Albert:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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I've tried: 2, 2.1.3, 2.1.4, the problem is still there. I don't
think the do_dssp is so difficult. just one command:<br>
<br>
do_dssp -s md.tpr -f md.trr -b 100 -e 200 -f ss.xpm<br>
<br>
<br>
On 03/30/2012 03:05 PM, Erik Marklund wrote:
<blockquote cite="mid:9FC2E7D7-75BC-4828-959F-3D4000BB75D6@xray.bmc.uu.se" type="cite">And what versions were those?
<div><br>
<div>
<div>30 mar 2012 kl. 15.06 skrev Albert:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>I've tried different kind of DSSP version, but the
problem is the same....<br>
<br>
<br>
On 03/30/2012 02:54 PM, <a moz-do-not-send="true" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>
wrote:<br>
<blockquote type="cite">Send gmx-users mailing list
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<blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><a moz-do-not-send="true" href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">When replying, please edit your
Subject line so it is more specific<br>
</blockquote>
<blockquote type="cite">than "Re: Contents of gmx-users
digest..."<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Today's Topics:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"> 1. Re: Re: do_dssp error (Erik
Marklund)<br>
</blockquote>
<blockquote type="cite"> 2. Re: Not able to continue
with Equilibration (Justin A. Lemkul)<br>
</blockquote>
<blockquote type="cite"> 3. Re: HB lifetime (Nidhi
Katyal)<br>
</blockquote>
<blockquote type="cite"> 4. Re: HB lifetime (Justin A.
Lemkul)<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">----------------------------------------------------------------------<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Message: 1<br>
</blockquote>
<blockquote type="cite">Date: Fri, 30 Mar 2012 13:28:05
+0200<br>
</blockquote>
<blockquote type="cite">From: Erik Marklund<<a moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>
</blockquote>
<blockquote type="cite">Subject: Re: [gmx-users] Re:
do_dssp error<br>
</blockquote>
<blockquote type="cite">To: Discussion list for GROMACS
users<<a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
</blockquote>
<blockquote type="cite">Message-ID:<<a moz-do-not-send="true" href="mailto:129A1E28-ABBD-4733-BA85-C1F6B2F4BE89@xray.bmc.uu.se">129A1E28-ABBD-4733-BA85-C1F6B2F4BE89@xray.bmc.uu.se</a>><br>
</blockquote>
<blockquote type="cite">Content-Type: text/plain;
charset="us-ascii"<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">And I replied "What's your dssp
version? The most recent ones have different flags that
are not yet supported by gromacs."<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Erik<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">30 mar 2012 kl. 13.23 skrev
Albert:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hello:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> there is some problem for my
do_dssp, it always claimed:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Program do_dssp_d, VERSION 4.5.5<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Source code file: do_dssp.c,
line: 572<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Fatal error:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Failed to execute command:
/usr/local/bin/dssp -na ddg1g7Id ddRwthIi>
/dev/null 2> /dev/null<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">someone suggest to compile
gromacs with double precision and I recompiled it with
--enable-double<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">but it still doesn't work.....<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">does anybody else have any
suggestions?<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">THX<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">-- <br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">gmx-users mailing list <a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><a moz-do-not-send="true" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Please search the archive at <a moz-do-not-send="true" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Please don't post (un)subscribe
requests to the list. Use the www interface or send it
to <a moz-do-not-send="true" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Can't post? Read <a moz-do-not-send="true" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">-----------------------------------------------<br>
</blockquote>
<blockquote type="cite">Erik Marklund, PhD<br>
</blockquote>
<blockquote type="cite">Dept. of Cell and Molecular
Biology, Uppsala University.<br>
</blockquote>
<blockquote type="cite">Husargatan 3, Box 596, 75124
Uppsala, Sweden<br>
</blockquote>
<blockquote type="cite">phone: +46 18 471 6688
fax: +46 18 511 755<br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true" href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-------------- next part
--------------<br>
</blockquote>
<blockquote type="cite">An HTML attachment was scrubbed...<br>
</blockquote>
<blockquote type="cite">URL: <a moz-do-not-send="true" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120330/7852dac3/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120330/7852dac3/attachment-0001.html</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">------------------------------<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Message: 2<br>
</blockquote>
<blockquote type="cite">Date: Fri, 30 Mar 2012 08:26:05
-0400<br>
</blockquote>
<blockquote type="cite">From: "Justin A. Lemkul"<<a moz-do-not-send="true" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
</blockquote>
<blockquote type="cite">Subject: Re: [gmx-users] Not able
to continue with Equilibration<br>
</blockquote>
<blockquote type="cite">To: Discussion list for GROMACS
users<<a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
</blockquote>
<blockquote type="cite">Message-ID:<<a moz-do-not-send="true" href="mailto:4F75A65D.1040701@vt.edu">4F75A65D.1040701@vt.edu</a>><br>
</blockquote>
<blockquote type="cite">Content-Type: text/plain;
charset=ISO-8859-1; format=flowed<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">francesca vitalini wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Dear Mark,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Thank you for your answer. I'm
trying now with the position restraints<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">and see what happens.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">However, another question came
up to my mind in the mean time. I'm<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">using GROMACS 3.3.1 (version
with mapping for reverse transformation,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">I have been posting on it
before) and for the mdrun the flag -coarse<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">is required. From the mdrun -h
help, the -coarse flag resulted to be a<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">generic trajectory, so I assumed
it was needed for the names of the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">atoms or something similar.
However, trying to run the nvt.mdp with<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the original coarse grained file
specified for this flag, resulted in<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the simulation not dying at the
very first steps.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> I'm not sure if it will work
out eventually ( the 20 ps simulations<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">is supposed to finish in 12
hours, which is still kind of worrying<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">despite my system being pretty
big) but definitely told me that the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">-coarse flag might be of
fundamental importance.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Unfortunately I couldn't find
any more detailed documentation about it.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Could anyone explain to me what
it does or point me to where to find<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the related documentation?<br>
</blockquote>
</blockquote>
<blockquote type="cite">Where did you obtain this version
of Gromacs? You're not using an official<br>
</blockquote>
<blockquote type="cite">version, so you're not likely to
find its documentation in the usual places and<br>
</blockquote>
<blockquote type="cite">it's very hard for this community
to help you using a modified version of<br>
</blockquote>
<blockquote type="cite">antiquated software. You're more
likely to have luck contacting whoever created<br>
</blockquote>
<blockquote type="cite">these modifications for help,
since potential problems with code stability and<br>
</blockquote>
<blockquote type="cite">performance are likely best
addressed by those who made the modifications.<br>
</blockquote>
<blockquote type="cite">Perhaps they are members of this
list, but contacting them directly is probably<br>
</blockquote>
<blockquote type="cite">a better approach.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-Justin<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
</div>
</blockquote>
</div>
<br>
<div> <span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; ">
<div>-----------------------------------------------</div>
<div>Erik Marklund, PhD</div>
<div>Dept. of Cell and Molecular Biology, Uppsala
University.</div>
<div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div>
<div>phone: +46 18 471 6688 fax: +46 18
511 755</div>
<div><a moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div>
<div><a moz-do-not-send="true" href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div>
</div>
</span></div>
</span></span> </div>
<br>
</div>
</blockquote>
<br>
<br>
</div>
-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists</blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
</div>
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