[gmx-users] pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 1 12:54:43 CEST 2009

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.


> 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


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