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<div align="left"><font face="Arial"><span style="font-size:10pt">Hallo!</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">The Problem with DPPC and the standard GROMACS forcefield is that for example the
bonds between CH3 and NL which are used to describe the ammonium-head of DPPC
are not defined within the forcefield (within ffgmxbn.itp if I am not mistaken).</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">I guess by the atomtype 'LC3' that you are using the dppc.itp from Tieleman's website.</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">He introduces some new atomtypes for the lipid-atoms which are not defined within the
forcefield. So you would have to include his lipid.itp within your topology, too.</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">However this file is incompatible to the new versions of GROMAX due to a second
[default] section.</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">A solution for this is to download the ffgmx_lipids.tar.gz from the topologies part from
the gromacs-homepage. It seems that the lipid.itp-Parameters are included in this
forcefield and it works fine with the popc.itp, dppc.itp, etc. from Tieleman's website.</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">(I took this information from a recent discussion within the gmx-users mailing list)</span></font></div>
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<div align="left"><font face="Arial"><span style="font-size:10pt">Link to forcefield-download: </span></font></div>
<div align="left"><font face="Arial" color="#0000ff"><span style="font-size:10pt"><u>http://www.gromacs.org/topologies/uploaded_force_fields/ffgmx_lipids.tar.gz</u></span></font><font
face="Arial"><span style="font-size:10pt"> </span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">(Thanks to Bert de Groot who uploaded this file!!!)</span></font></div>
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<div align="left"><font face="Arial"><span style="font-size:10pt">If you want to use a different forcefield you will probably have to explicitly declare the
atomtypes, bonds, etc. you are using within the dppc.itp / your own lipid.itp / the
[forcefield].atp or stick to those already implemented within the forcefield. (I think the
modified ffgmx43a2-forcefield uses LCH2 and LCH3 to describe the aliphatic chains but
I am not sure)</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">I hope this is of some help to you.</span></font></div>
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<div align="left"><font face="Arial"><span style="font-size:10pt">Steffen</span></font></div>
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<div align="left"><font face="Arial"><span style="font-size:10pt">On 15 Jul 2004 at 13:28, Dinesh Pinisetty wrote:</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> Hi everyone,</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">>        As christopher told I tried all permutations
and combinations</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> arranging the #include files,when I used #include lipid.itp,#include</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> ffG43a1.itp,#include dppc.itp in this order now I am getting error as</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> Atomtype 'C' is missing only the atom name is changed rest all is the same.</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> when I used ffG43a1,dppc.itp,lipid.itp 'LC3' atomtype was missing and when</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> I used ffG43a1.itp,lipid.itp and dppc.itp I was getting error as 'LC3'</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> atomtype was missing.I do not think mistake is in there.</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">>  Please suggest me what to do now.............</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> Thanks in advance........</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> It may do with the order that you included your itp files in your top file.</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> If</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> the atom definitions for DPP are in lipid.itp, then make sure lipid.itp is</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> included before dppc.itp.</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> Also, have you checked out Tieleman's site for lipid coordinate and</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> topology</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> files?</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> Christopher Tran</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> chr.tran@utoronto.ca</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> Quoting Dinesh Pinisetty <dpinis1@lsu.edu>:</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> ></span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> ></span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> ></span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> ></span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > Hello everybody,</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> >           I have been trying to
run MD simulation for dppc membrane with</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > water molecules.Intially when I run pdb2gmx for .top and .gro files it</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> gave</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > me an error saying that the residue DPP was not there in residue topology</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > database.Then I created my own dppc.itp file and lipid.itp file and added</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > it to the incomplete .top file created by pdb2gmx.I created .gro file by</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > editconf.When I run grompp I am getting an error as</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> >           processi
ng topology</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > Generated 279 of the 1225 non-bonded parameter combinations</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > Cleaning up temporary file gromppG9xnJE</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > Fatal error:Atomtype 'LC3' not found</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > But I have this atom present in dppc.itp and even added in ffG43a1.atp as</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> I</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > was using ffG43a1 force field.Should I add anything more anywhere.</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > Please let me know where I might have made a mistake.</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > Thanks a lot in advance..................</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> ></span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> > Dinesh........</span></font></div>
<div align="left"><font face="Arial" color="#007f00"><span style="font-size:10pt">> ></span></font></div>
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