<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi Gmx users,<br><br> Are we able to run both the lower and higher version at a time?<br>If possible, please help me how to do it.<br><br>with thanks<br><br><br><br>*******************************+ <br>
Dr.Karunakaran Chandran +<br>
Biophysics Department + <br>
Medical College of Wisconsin +<br>
Milwaukee, WI-53226 +<br>
Resi.: 414-443-0085 +<br>
Off : 414-456-4034 +<br>
********************************<br><br>--- On <b>Tue, 30/8/11, gmx-users-request@gromacs.org <i><gmx-users-request@gromacs.org></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: gmx-users-request@gromacs.org <gmx-users-request@gromacs.org><br>Subject: gmx-users Digest, Vol 88, Issue 168<br>To: gmx-users@gromacs.org<br>Date: Tuesday, 30 August, 2011, 7:25 AM<br><br><div class="plainMail">Send gmx-users mailing list submissions to<br> <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>or, via email, send a message with subject or body 'help' to<br> <a
ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br><br>You can reach the person managing the list at<br> <a ymailto="mailto:gmx-users-owner@gromacs.org" href="/mc/compose?to=gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. g_lie (pawan raghav)<br> 2. Re: OPLS-AA Unknown Atomtype (Yao Yao)<br> 3. Re: OPLS-AA Unknown Atomtype (Justin A. Lemkul)<br> 4. MARTINI / all-atom mapping (Michael Daily)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 29 Aug 2011 20:49:40 +0530<br>From: pawan raghav <<a ymailto="mailto:pwnrghv@gmail.com"
href="/mc/compose?to=pwnrghv@gmail.com">pwnrghv@gmail.com</a>><br>Subject: [gmx-users] g_lie<br>To: <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <CAD+UPv=7dRaYchD1i89T9C4QRfaNcAkYKHngkGdC=<a ymailto="mailto:D2bCsRKtQ@mail.gmail.com" href="/mc/compose?to=D2bCsRKtQ@mail.gmail.com">D2bCsRKtQ@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>g_lie calculates the deltaG= alpha(<Vl-s LJ>p - <Vl-s LJ>w) + beta(<Vl-s<br>el>p - <Vl-s el>w) equation. But when calculating DGbind from g_lie it will<br>ask for only one term at a time i.e. -Elj for either <Vl-s LJ>p or <Vl-s<br>LJ>w and -Cqq for either <Vl-s el>p or <Vl-s el>w. My question is when<br>using only <Vl-s LJ>p for -Elj and Vl-s el>p for -Cqq, how the LJ and EL<br>terms calculated for ligand-water
interaction or in vice-versa condition for<br>ligand-protein interactions to complete the deltaG equation?<br><br>-- <br>Pawan<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110829/c32d8291/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110829/c32d8291/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 29 Aug 2011 12:29:39 -0700 (PDT)<br>From: Yao Yao <<a ymailto="mailto:yao0o@ymail.com" href="/mc/compose?to=yao0o@ymail.com">yao0o@ymail.com</a>><br>Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype<br>To: "<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>" <<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>>, Discussion list for
GROMACS<br> users <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a ymailto="mailto:1314646179.30982.YahooMailNeo@web120404.mail.ne1.yahoo.com" href="/mc/compose?to=1314646179.30982.YahooMailNeo@web120404.mail.ne1.yahoo.com">1314646179.30982.YahooMailNeo@web120404.mail.ne1.yahoo.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>HI Justin,<br><br>I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions.<br><br>So I do not think ions addition will help. And I double-checked the angles, bonds, .... mentioned in the ffoplsaabon.itp, they are there.<br>So I do not know any other files I may need to modify.<br><br>Thanks,<br><br>yao<br><br><br><br><br>________________________________<br>From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu"
href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>><br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Sent: Monday, August 29, 2011 3:41 AM<br>Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype<br><br><br><br>Yao Yao wrote:<br>> Hi Justin,<br>> <br>> Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp,<br>> but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like,<br>> <br>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>> checking input for internal consistency...<br>> processing topology...<br>> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp<br>> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp<br>> Opening library file
/share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp<br>> Generated 338253 of the 338253 non-bonded parameter combinations<br>> Generating 1-4 interactions: fudge = 0.5<br>> Generated 338253 of the 338253 1-4 parameter combinations<br>> <br>> ERROR 1 [file cro.top, line 37]:<br>> No default Bond types<br>> <br>> <br>> ERROR 2 [file cro.top, line 71]:<br>> No default Angle types<br>> <br>> <br>> ERROR 3 [file cro.top, line 72]:<br>> No default Angle types<br>> <br>> <br>> ERROR 4 [file cro.top, line 85]:<br>> No default Angle types<br>> <br>> <br>> ERROR 5 [file cro.top, line 91]:<br>> No default Ryckaert-Bell. types<br>> <br>> <br>> ERROR 6 [file cro.top, line 92]:<br>> No default Ryckaert-Bell. types<br>> <br>> <br>> ERROR 7 [file cro.top, line 93]:<br>> No default
Ryckaert-Bell. types<br>> <br>> <br>> ERROR 8 [file cro.top, line 108]:<br>> No default Ryckaert-Bell. types<br>> <br>> <br>> ERROR 9 [file cro.top, line 112]:<br>> No default Proper Dih. types<br>> <br>> <br>> ERROR 10 [file cro.top, line 113]:<br>> No default Proper Dih. types<br>> <br>> <br>> ERROR 11 [file cro.top, line 114]:<br>> No default Proper Dih. types<br>> <br>> Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp<br>> Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp<br>> Excluding 3 bonded neighbours molecule type 'Protein'<br>> Excluding 2 bonded neighbours molecule type 'SOL'<br>> Excluding 2 bonded neighbours molecule type 'SOL'<br>> <br>> NOTE 1 [file cro.top, line 142]:<br>> System has non-zero total charge: -1.022478e+00<br>> <br><br>This total charge
suggests that your topology is badly broken.<br><br>> <br>> processing coordinates...<br>> double-checking input for internal consistency...<br>> renumbering atomtypes...<br>> converting bonded parameters...<br>> <br>> There was 1 note<br>> <br>> -------------------------------------------------------<br>> Program grompp, VERSION 4.0.7<br>> Source code file: grompp.c, line: 986<br>> <br>> Fatal error:<br>> There were 11 errors in input file(s)<br>> -----------------------------------------------<br>> <br>> I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values?<br>> <br><br>If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again.<br><br>-Justin<br><br>--
========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110829/328ad1ea/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110829/328ad1ea/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 29 Aug 2011 15:50:45 -0400<br>From: "Justin A. Lemkul" <<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype<br>To: Discussion list for GROMACS users <<a
ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a ymailto="mailto:4E5BED95.4010803@vt.edu" href="/mc/compose?to=4E5BED95.4010803@vt.edu">4E5BED95.4010803@vt.edu</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br><br><br>Yao Yao wrote:<br>> HI Justin,<br>> <br>> I met these errors when I grompp to do 1st-time energy minimization <br>> before I planned to add the ions.<br>> So I do not think ions addition will help. And I double-checked the<br><br>The net charge problem cannot be solved by adding ions. A fractional charge of <br>that magnitude indicates the charges in the topology are wrong.<br><br>> angles, bonds, .... mentioned in the ffoplsaabon.itp, they are there.<br>> So I do not know any other files I may need to modify.<br>> <br><br>The only file that contains [bondtypes], [angletypes], etc is
ffoplsaabon.itp, <br>so if the entries are indeed there, have the correct format, and are placed <br>appropriately, you wouldn't be getting this error. So unless you post the exact <br>lines in their exact context, I'm left to assume that you've done something else <br>wrong.<br><br>-Justin<br><br>> Thanks,<br>> <br>> yao<br>> <br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Monday, August 29, 2011 3:41 AM<br>> *Subject:* Re: [gmx-users] OPLS-AA Unknown Atomtype<br>> <br>> <br>> <br>> Yao Yao wrote:<br>> > Hi Justin,<br>> ><br>> >
Thanks for your last reply. Now it seems that OPLS has known the <br>> atomtypes after I added those CA1, ... to ffoplsaanb.itp,<br>> > but after I claim all the angles, dihedrals, ... in the <br>> ffoplsaabon.itp, it still gives errors like,<br>> ><br>> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>> > checking input for internal consistency...<br>> > processing topology...<br>> > Opening library file <br>> /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp<br>> > Opening library file <br>> /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp<br>> > Opening library file <br>> /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp<br>> > Generated 338253 of the 338253 non-bonded parameter combinations<br>> > Generating 1-4 interactions: fudge = 0.5<br>> > Generated 338253 of the 338253
1-4 parameter combinations<br>> ><br>> > ERROR 1 [file cro.top, line 37]:<br>> > No default Bond types<br>> ><br>> ><br>> > ERROR 2 [file cro.top, line 71]:<br>> > No default Angle types<br>> ><br>> ><br>> > ERROR 3 [file cro.top, line 72]:<br>> > No default Angle types<br>> ><br>> ><br>> > ERROR 4 [file cro.top, line 85]:<br>> > No default Angle types<br>> ><br>> ><br>> > ERROR 5 [file cro.top, line 91]:<br>> > No default Ryckaert-Bell. types<br>> ><br>> ><br>> > ERROR 6 [file cro.top, line 92]:<br>> > No default Ryckaert-Bell. types<br>> ><br>> ><br>> > ERROR 7 [file cro.top, line 93]:<br>> >
No default Ryckaert-Bell. types<br>> ><br>> ><br>> > ERROR 8 [file cro.top, line 108]:<br>> > No default Ryckaert-Bell. types<br>> ><br>> ><br>> > ERROR 9 [file cro.top, line 112]:<br>> > No default Proper Dih. types<br>> ><br>> ><br>> > ERROR 10 [file cro.top, line 113]:<br>> > No default Proper Dih. types<br>> ><br>> ><br>> > ERROR 11 [file cro.top, line 114]:<br>> > No default Proper Dih. types<br>> ><br>> > Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp<br>> > Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp<br>> > Excluding 3 bonded neighbours molecule type 'Protein'<br>> > Excluding 2 bonded neighbours molecule type
'SOL'<br>> > Excluding 2 bonded neighbours molecule type 'SOL'<br>> ><br>> > NOTE 1 [file cro.top, line 142]:<br>> > System has non-zero total charge: -1.022478e+00<br>> > <br>> <br>> This total charge suggests that your topology is badly broken.<br>> <br>> ><br>> > processing coordinates...<br>> > double-checking input for internal consistency...<br>> > renumbering atomtypes...<br>> > converting bonded parameters...<br>> ><br>> > There was 1 note<br>> ><br>> > -------------------------------------------------------<br>> > Program grompp, VERSION 4.0.7<br>> > Source code file: grompp.c, line: 986<br>> ><br>> > Fatal error:<br>> > There were 11 errors in input file(s)<br>> >
-----------------------------------------------<br>> ><br>> > I do double-check those bondtypes, angles, and interactions mentioned <br>> in the errors, and I am pretty sure I have already declared those values <br>> in the ffoplsaabon.itp. Is there any other file I also need to mention <br>> those values?<br>> ><br>> <br>> If these types were actually present in ffoplsaabon.itp, then you <br>> wouldn't get these errors. Double check again.<br>> <br>> -Justin<br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a> <br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www <br>> interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <br>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> <br>> <br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br>------------------------------<br><br>Message: 4<br>Date: Mon, 29 Aug 2011 18:55:09 -0700<br>From:
Michael Daily <<a ymailto="mailto:mdaily.work@gmail.com" href="/mc/compose?to=mdaily.work@gmail.com">mdaily.work@gmail.com</a>><br>Subject: [gmx-users] MARTINI / all-atom mapping<br>To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <CAF-wSYEuyxzu7za2DKy1-E+<a ymailto="mailto:xJeWb3UgC4x9TU3XTZwoi-Os_Dw@mail.gmail.com" href="/mc/compose?to=xJeWb3UgC4x9TU3XTZwoi-Os_Dw@mail.gmail.com">xJeWb3UgC4x9TU3XTZwoi-Os_Dw@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi all,<br><br>I am trying to reverse-map some martini lipids to united atom. In order to<br>do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I<br>cannot find this, only an imprecise graphic, in the MARTINI paper; the<br>martini.itp file doesn't appear to list which heavy atoms are
represented by<br>each CG bead either. For example, I'm looking for something like:<br><br>'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'],<br> 'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'],<br> 'GL1' : ['C13', 'O14', 'C15', 'O16'],<br> 'GL2' : ['C32', 'O33', 'C34', 'O35'],<br><br>etc.<br><br>For some atoms it's obvious which MARTINI groups they belong in, but others<br>on the borderline are not obvious. For example, does C12 belong in PO4 or<br>GL1?<br><br>Anybody have a master list like this?<br><br>Thanks,<br>Mike<br><br>-- <br>====================================<br>Michael D. Daily<br>Postdoctoral research associate<br>Pacific Northwest National Lab (PNNL)<br>509-375-4581<br>(formerly Qiang Cui group, University of Wisconsin-Madison)<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a
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