AMBER Archive (2009)

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

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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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• Previous message: Antonija Tomić: "[AMBER] mm_pbsa-Binding and Stability tests?"
• In reply to: Catein Catherine: "[AMBER] Is it the correct procedures to strip water for MM/GBSA calculations?"
• Next in thread: Carlos Simmerling: "Re: [AMBER] How to strip water for MM/GBSA calculations?"
• Next in thread: Catein Catherine: "[AMBER] Can I do DNA bending with AMBER?"
• Reply: Carlos Simmerling: "Re: [AMBER] How to strip water for MM/GBSA calculations?"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]