[gmx-users] problem with pdb2gmx

[Nizar Masbukhin]

i wrote this

pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce

On May 1, 2014, at 5:28 PM, Chandan Choudhury <iitdckc at gmail.com> wrote:

> On Thu, May 1, 2014 at 3:32 PM, Nizar Masbukhin <nizar.fkub08 at gmail.com>wrote:
> 
>> Hi, friends. I’m new to gromacs. I’m trying to learn it based on
>> tutorial
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
>> .
>> Whenever i input pdb2gmx line, i always get this message:
>> 
>> Using the Oplsaa force field in directory oplsaa.ff
>> 
>> Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/
>> aminoacids.r2b
>> Reading 1AKI.pdb...
>> 
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.5.5
>> Source code file: futil.c, line: 491
>> 
>> File input/output error:
>> 1AKI.pdb
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> 
>> What is wrong? can anyone explain? and what is the solution?
>> 
> 
> Please copy and paste your command.
> 
> It seems that there is some problem in the pdb file (1AKI). You can check
> its contents.
> 
> Chandan
> 
>> 
>> Thank for your help
>> --
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> 
> 
> 
> -- 
> 
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
> -- 
> Gromacs Users mailing list
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