<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><span style="font-family: times new roman,new york,times,serif;">On </span><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2">Sat, Jan. 22, 2011 at 1:44 AM, </font><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2">Sweta Iyer <iyer@wehi.EDU.AU> wrote:</font><font face="Tahoma" size="2"><span style="font-family: times new roman,new york,times,serif;"></span><br></font><div> <br>> > On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <<a href="mailto:iyer@wehi.EDU.AU">iyer@wehi.EDU.AU</a>> wrote:<br>> >> Hi, I am trying to generate topology files for a set of lipids with the<br>> >> help of topolbuild1_3.tgz package found at the other software page of<br>> >> GROMACS website.<br>>
>><br>> >> I downloaded and installed all files and tried running the program with<br>> >> a<br>> >> MOL2 file with charges in it. However, it shows an error message as<br>> >> follows:<br>> >><br>> >> Fatal error.<br>> >> Source code file: readmol2.c, line: 758<br>> >> Atom 1 (C) has 3 connections when allowed 0<br>> >><br>> >> I am not sure how to get over this problem! Wonder what will fix this<br>> >> error and get the program running!<br>> ><br>> > A major requirement of topolbuild is that the mol2 file use correct atom<br>> > types as defined by Tripos, whose file format mol2 is, and as used in<br>> > Sybyl.<br>> > The error message suggests that you have not specified correct Tripos<br>> > Sybyl<br>> > atom types. There may be other problems in your mol2 file as well.<br>> > Correct the
atom types and check that the file is otherwise syntactically<br>> > correct and it should work.<br>> ><br>> > However, I believe that lipid topology files for gromacs are already available<br>> > for download.<br>> ><br>> > I hope that helps.<br>> <br>> Hi Bruce,<br>> Thanx for the reply. The MOL2 file was generated by the RESP ESP charge<br>> derive server. I did not check the file in SYBYL. However, structurally it<br>> seems correct. I will try reading it into sybyl and then resave it into<br>> another mol2 file.<br><br>I am not familiar with that server. However, a Sybyl atom type for most<br>atoms consists of the atomic symbol followed by a period followed by<br>a number or a short character string. For example, C.3 is an sp3 hybridized<br>carbon, N.ar is an aromatic ring nitrogen, and O.co2 is a carboxylic acid<br>oxygen. I believe the file you have lacks the type designator
after the atomic<br>symbol for atom 1.<br><br>> I am looking at making topology files for lipids like cardiolipin, di<br>> myristoyl phosphatidylethanolamine, dimyristoyl phosphatidylinositol and<br>> myristoleic acid. DO you know of any available gromacs topology files for<br>> these?<br><br>I cannot help you on that, but would suggest you ask those who have<br>published lipid simulations.<br><br></div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 10pt;"><br><div style="font-family: Courier New,monaco,monospace,sans-serif; font-size: 10pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Sweta Iyer <iyer@wehi.EDU.AU><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span
style="font-weight: bold;">Sent:</span></b> Sat, January 22, 2011 1:44:25 AM<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Re: Problem with using topolbuild1_3.tgz<br></font><br><br>> Date: Fri, 21 Jan 2011 06:55:30 -0800 (PST)<br>> From: "Bruce D. Ray" <<a ymailto="mailto:brucedray@yahoo.com" href="mailto:brucedray@yahoo.com">brucedray@yahoo.com</a>><br>> Subject: Re: [gmx-users] Problem with using topolbuild1_3.tgz<br>> To: <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Message-ID: <<a ymailto="mailto:417950.70449.qm@web35801.mail.mud.yahoo.com" href="mailto:417950.70449.qm@web35801.mail.mud.yahoo.com">417950.70449.qm@web35801.mail.mud.yahoo.com</a>><br>> Content-Type: text/plain; charset="us-ascii"<br>><br>> On Thu, January 20, 2011 at 6:41PM, Sweta Iyer <<a ymailto="mailto:iyer@wehi.EDU.AU"
href="mailto:iyer@wehi.EDU.AU">iyer@wehi.EDU.AU</a>> wrote:<br>>> Hi, I am trying to generate topology files for a set of lipids with the<br>>> help of topolbuild1_3.tgz package found at the other software page of<br>>> GROMACS website.<br>>><br>>> I downloaded and installed all files and tried running the program with<br>>> a<br>>> MOL2 file with charges in it. However, it shows an error message as<br>>> follows:<br>>><br>>> Fatal error.<br>>> Source code file: readmol2.c, line: 758<br>>> Atom 1 (C) has 3 connections when allowed 0<br>>><br>>> I am not sure how to get over this problem! Wonder what will fix this<br>>> error and get the program running!<br>><br>> A major requirement of topolbuild is that the mol2 file use correct atom<br>> types as defined by Tripos, whose file format mol2 is, and as used in<br>> Sybyl.<br>> The error message
suggests that you have not specified correct Tripos<br>> Sybyl<br>> atom types. There may be other problems in your mol2 file as well.<br>> Correct the atom types and check that the file is otherwise syntactically<br>> correct and it should work.<br>><br>> However, I believe that lipid topology files for gromacs are already<br>> available<br>> for download.<br>><br>> I hope that helps.<br>><br>><br>> --<br>> Bruce D. Ray, Ph.D.<br>> Associate Scientist<br>> IUPUI<br>> Physics Dept.<br>> 402 N. Blackford St.<br>> Indianapolis, IN 46202-3273<br><br>Hi Bruce,<br>Thanx for the reply. The MOL2 file was generated by the RESP ESP charge<br>derive server. I did not check the file in SYBYL. However, structurally it<br>seems correct. I will try reading it into sybyl and then resave it into<br>another mol2 file.<br>I am looking at making topology files for lipids like cardiolipin, di<br>myristoyl
phosphatidylethanolamine, dimyristoyl phosphatidylinositol and<br>myristoleic acid. DO you know of any available gromacs topology files for<br>these?<br><br>Cheers<br>Sweta<br>><br>><br>><br>><br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL:<br>> <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/bdd5ae9c/attachment.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/bdd5ae9c/attachment.html</a><br>><br>> ------------------------------<br>><br>> --<br>> gmx-users mailing list<br>> <a ymailto="mailto:gmx-users@gromacs.org" href="mailto: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
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