Hi gromacs users,
I am using the gromacs 4.5.3 version. I created a lipopetide which consist of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp (residues) using ARGUSLAB and I saved it as a pdb file. Then, when I used the following command in gromacs: pdb2gmx –f lipopepArgus.pdb (GROMOS96 45a3 force field&spc type water model) I got the following error message: Fatal error: Residue 'DEF' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors As far as I could understand, there is no problem with the residues but there is a problem with the atoms in the tail (12 Carbon atoms, 23 Hydrogen atoms and an Oxygen atom, actually it is called a lauroic acid). These atoms are defined as DEF. I thought I should rename the pdb to the expected name given in the .rtp file of the 45a3 force field for my lipopeptide. But I could not find a parameterization for the lauroic acid. In this case, what shoul I do? At the http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blockspage, I found; *Abbrev.* *Source* *2* *Full Name* *Formula* *Specifics* LAU fa.itp O lauroic acid C11H23COOH - Does using fa.itp file solve my problem? If yes, where can I get this file? I would be so glad if you can help me solve this problem. Thank you in advance, Deniz
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