Re: [AMBER] Restrain with PMEMD

From: Ross Walker <>
Date: Tue, 6 Jul 2010 09:19:30 -0700

Hi Giovanni,

Yes you can run these types of restraints with PMEMD. The only difference is
you have to use the old style group input in place of the restraint mask
input. However, you can use the program $AMBERHOME/exe/ambmask to translate
a mask into the old style group input.

Good luck,


> -----Original Message-----
> From: Giovanni Doni []
> Sent: Tuesday, July 06, 2010 9:08 AM
> To:
> Subject: [AMBER] Restrain with PMEMD
> Dear all,I'm wondering about the possibility to run a simulation with
> restrains (I mean bond with armonic law) on some amino acids' position
> with Pmemd; I'm doing that thing with sander but it takes very long
> time due to the dimension of the sistem. Are there ani command to
> implement this solution with pmemd or not? Thanks a lot
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Received on Tue Jul 06 2010 - 09:30:04 PDT
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