AMBER Archive (2009)

Subject: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Aug 11 2009 - 06:10:09 CDT

Dear Sir/Madam,

 

I have done the MD simulations for a TIP3P and implicit solvent system. After done, I do MM-GBSA analysis for both systems with or without nm calculations.

 

I can get implicit solvent system done without error message. However, for the TIP3P system, I can only finish the without nm calculation analysis. Everytime I do the nm calculation for the TIP3P system, following error message appears.

 

/amber8/exe/nmode -O -i nmode_com.in -o nmode_com.1.out -c sanmin_com.1.restrt -p ../cpt_ser_complex2.prmtop not running properly

 

I tried to decrease the number of crd files from 100 to 1, so that the memory error posted in the website could not be a problem in this test case. However, the same error message appear.

 

I know previous users has also face the same problems, it seems to related to bugs in MM-GBSA, however, since the implicit solvent system can be done, it suspect it is due to other unknow reasons. Could anyone help?

 

Best regards,

Cat

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