[gmx-users] Fatal error: Atomtype 'K' not found!

Tue Oct 18 04:14:41 CEST 2005

Because I will include decane as solvent and I don't have topology file for decane. Or I should build one. Thanks for your comment.

mao  
> 
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> Hi,
> 
> 
> > I was using Gromacs-3.2-1 for peptide simulations. I first used  
> > "pdb2gmx" to generate .gro file and I chose 5 from the following  
> > options to include H
> > "Select the Force Field:
> >  0: GROMOS96 43a1 Forcefield (official distribution)
> >  1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
> >  2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
> >  3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> >  4: Gromacs Forcefield (see manual)
> >  5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new  
> > runs)"
> 
> Question: I assume you read the entire last line here. Why do you  
> need to use ffgmx2 and not e.g. OPLS?
> 
> Cheers,
> 
> Erik
> 
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
> 
> 
> 
> 
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> <HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
> -khtml-line-break: after-white-space; "><DIV><BLOCKQUOTE =
> type=3D"cite"></BLOCKQUOTE><DIV><FONT class=3D"Apple-style-span" =
> color=3D"#0000DD">Hi,</FONT></DIV><BR><BR><BLOCKQUOTE type=3D"cite"><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "></DIV><DIV style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I was =
> using Gromacs-3.2-1 for peptide simulations. I first used "pdb2gmx" to =
> generate .gro file and I chose 5 from the following options to include =
> H</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: =
> 0px; margin-left: 0px; ">"Select the Force Field:</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</SPAN>0: =
> GROMOS96 43a1 Forcefield (official distribution)</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</SPAN>1: =
> GROMOS96 43b1 Vacuum Forcefield (official distribution)</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</SPAN>2: =
> GROMOS96 43a2 Forcefield (development) (improved alkane =
> dihedrals)</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; "><SPAN =
> class=3D"Apple-converted-space">=A0</SPAN>3: OPLS-AA/L all-atom force =
> field (2001 aminoacid dihedrals)</DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN =
> class=3D"Apple-converted-space">=A0</SPAN>4: Gromacs Forcefield (see =
> manual)</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; "><SPAN =
> class=3D"Apple-converted-space">=A0</SPAN>5: gmx Forcefield with =
> hydrogens for NMR stuff (Do NOT use for new =
> runs)"</DIV></BLOCKQUOTE></DIV><DIV><FONT class=3D"Apple-style-span" =
> color=3D"#0000DD"><BR =
> class=3D"khtml-block-placeholder"></FONT></DIV>Question: I assume you =
> read the entire last line here. Why do you need to use ffgmx2 and not =
> e.g. OPLS?<DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Erik<DIV><DIV><BR><DIV> =
> <SPAN class=3D"Apple-style-span" style=3D"border-collapse: separate; =
> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; =
> font-size: 12px; font-style: normal; font-variant: normal; font-weight: =
> normal; letter-spacing: normal; line-height: normal; text-align: auto; =
> -khtml-text-decorations-in-effect: none; text-indent: 0px; =
> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; =
> white-space: normal; widows: 2; word-spacing: 0px; =
> "><DIV>-----------------------------------------------------------</DIV><D=
> IV>Erik Lindahl=A0 &lt;<A =
> href=3D"mailto:lindahl at sbc.su.se">lindahl at sbc.su.se</A>&gt;</DIV><DIV>Assi=
> stant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm =
> University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564=A0 =A0 =
> =A0Fax: +46 8 5537 8214</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><BR =
> class=3D"Apple-interchange-newline"></SPAN> =
> </DIV><BR></DIV></DIV></DIV></BODY></HTML>=
> 
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