[gmx-users] grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr

Yang Ye leafyoung at yahoo.com
Thu Aug 16 04:04:47 CEST 2007

On 8/16/2007 9:53 AM, Mark Abraham wrote:
> huifang liu wrote:
>> I typed this command:   grompp -f em.mdp -c speptide.pdb -p 
>> \#spetide.top.1#\ -o speptide_em.tpr
>>  It responded to me like this:Invalid command line argument:
>> speptide_empdb.tpr
>> I am a new -learner.Can you tell me where the problem is.
> Backslashes are used to "escape" characters to which your shell would 
> otherwise assign a special meaning. Depending on your shell "#" might 
> start a comment, so to prevent that, you use a backslash before it, in 
> order to let the shell know you really want that character. Putting a 
> backslash before a space doesn't do you any good...
> Mark
On top of Mark's point, many programs in GROMACS uses suffix to 
determine the file type. To use those files with name beginning #, you 
shall remove the leading and trailing # in the filename by renaming.
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