AMBER Archive (2009)

Subject: [AMBER] How to strip water for MM/GBSA calculations?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri Aug 21 2009 - 05:38:27 CDT


Dear All,

 

Could you mind to let me know if it is necessary to strip water from the mdcrd files before extracting snapshot for MM/GBSA calculation? If yes, could you mind to let me know if it is the correct ptraj file to be use?

 

> trajin xxx.mdcrd
>
> trajout xxx_strip.mdcrd
>
> strip :WAT

 

Best regards & many thanks in advanced,

 

Cat
 

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