[AMBER] Thermodynamic Integration by using pmemd

From: Sun <sunbintyy.163.com>
Date: Fri, 11 Jul 2014 17:33:21 +0800 (CST)

Dear All,
I want to use pmemd ( Amber version 14 £İto perform a thermodynamic integration (TI ) to calculate the free energy of one process. According to the Amber14 Reference Manual, when the pmemd is used, only one set of topology and coordinate files is needed, while in the mutisander TI calculation, two sets of topology and coordination files corresponding to the start point and end point are needed.

In my calculation by using pmemd, the system contains 120 residues ( 100 regular amino acids and 20 waters ). The atom numbers are unchanged in the start point and end point . When I combined these two structures (pdb) into one pdb and then used Leap to generate topology and coordinate files, I found that , by default , Leap put all water molecules in the last place, e.g. :1-200 are amimo acids and :200-240 are water molecules. But what I actually expect is the oder like this : :1-120 are amino acids and water molecules corresponding to the start pont and :121-240 are the end points.

So how should I do to make the order of resudes as what I want when using Leap to generate the topology and coordinate files ?

Thanks in advance !


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Received on Fri Jul 11 2014 - 03:00:02 PDT
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