[gmx-users] Merge + CHARMM?

[Justin A. Lemkul]

Alessandro.Maiorana at roma2.infn.it wrote:
> Hi,
> 
> I am trying to use the CHARMM27 force field to Gromacs to simulate two
> proteins unite with command -merge, but the following error message is
> coming:
> "Opening library file
> /storage2/rgr/software/gromacs/share/gromacs/top/aminoacids.dat
> 
> WARNING: atom C is missing in residue LYSH 16 in the pdb file
> 
> 
> WARNING: atom C is missing in residue LYSH 32 in the pdb file
> 
> 
> -------------------------------------------------------
> Program pdb2gmx_d, VERSION 3.3.3
> Source code file: pdb2top.c, line: 697
> 
> Fatal error:
> There were 2 missing atoms in molecule Protein_A, if you want to use this
> incomplete topology anyhow, use the option -missing
> -------------------------------------------------------"
> 
> Can you help me? See you soon.
> 

http://oldwiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms

-Justin

> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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