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-
[n...@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.
<snip>
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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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