[gmx-users] problem in creating .gro file

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 2 13:27:21 CET 2009

nitu sharma wrote:
> Dear All,
>                        I have successfully installed gromacs -4.0.3 on 
> my linux fedora core-8 i686 32 bit computer but  I was not able to 
> source the GMXRC script because in my system only "bash shell" is 
> active  so I want to know is C-shell must needed to run gromacs 
> successfully? Because  I am facing one problem i.e .gro file doesn't 
> created  when i put the command to create .gro and .top file
> .the .top file and topol .top file is created but .gro file cant be 
> created , the command line and output is like this-
> [nitu at localhost mdtap]$ pdb2gmx -f rr1.pdb -p rr1.top -o rr1.gro

 From GMXRC:

# This is a convenience script to determine which
# type of shell you have, and then run GMXRC.[csh|bash|zsh]
# from the Gromacs binary directory.
# If you only use one shell you can copy that GMXRC.* instead.

So if you have bash, then the solution should be straightforward.


> WARNING: atom OH is missing in residue TYR 535 in the pdb file
> WARNING: atom HH is missing in residue TYR 535 in the pdb file
>          You might need to add atom HH to the hydrogen database of 
> residue TYR
>          in the file ff???.hdb (see the manual)
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.3
> Source code file: pdb2top.c, line: 704
> Fatal error:
> There were 2 missing atoms in molecule Protein_A, if you want to use 
> this incomplete topology anyhow, use the option -missing
> -------------------------------------------------------
> "The World is a Friendly Place" (Magnapop)
> How can I use missing option and can be able to create .gro file  could 
> anybody help me in doing my work becoz I just started working with 
> gromacs so i am facing these type of problems

Do not use the -missing option.  You have an incomplete .pdb file, so you will 
have to use some external software (DeepView, Modeller, etc) to fix your structure.


> plese if possible than anybody help me.
> Thank you very much for taking out of your time for my consideration.
> Nitu Sharma
> Structural Biology lab
> School Of Life sciences
> Jawaherlal Nehru University
> New Delhi, India
> ------------------------------------------------------------------------
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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