[gmx-users] problem with pdb2gmx

[Chandan Choudhury]

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