Asmaa Elsheshiny wrote:
Dear All,
I tried to use the following command line
pdb2gmx -f -i brady.pdb -o brady.gro -p brady.top -ignh
But I get the following error massage
File input/output error:
eiwit.pdb
So I tried to modify aminoacides.dat to include all the required aminoacids
residues but , I failed because these files are readonly .
So, How can I fix this problem.
You supplied the -f flag with no associated filename, so Gromacs is going to
assume the default file "eiwit.pdb" is present in the working directory. No
need to change system-level files, just supply an input. I think you tried this
with the -i flag, which is wrong. Read the manual and/or pdb2gmx -h.
-Justin
Cheers,
Asmaa
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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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