[AMBER] Using TIP4PEW amber FF in NAMD

From: <peter.schmidtke.discngine.servier.com>
Date: Fri, 24 Jul 2015 08:27:34 +0000

Dear Amber users,

I am trying to port a few MD preparation scripts using the TIP3 water model to TIP4EW. Note that currently the final MD's are run using NAMD 2.10 and not pmemd. As soon as I start a minimization using NAMD I run into errors like :
FATAL ERROR: Hydrogen group error caught in rattle1().

I guess that the lone pair is not considered correctly within NAMD. Hereafter steps I used to prepare the system and a sample NAMD input file excerpt.

Leap :
        Source leaprc.ff14SB
        loadAmberParams frcmod.tip4pew
        loadAmberParams frcmod.ionsjc_tip4pew
        set default FlexibleWater on
        system=loadPdb system.pdb
        #next adding counter ions, solvating using TIP4PEWBOX ...
        saveAmberParm system system_solvated.prmtop system_solvated.prmcrd

Running this using the last version of tleap actually creates the topology, but issues output I'm not quite used to, namely hundreds of lines like :

        "1-4: angle 56188 56189 duplicates bond ('triangular' bond) or angle ('square' bond)"
 I googled this up and found that this warning can be ignored, can you confirm?

Next I want to minimize the system using NAMD. I thus used the following input (I just kept the most relevant part for the water model here):

        coordinates system_solvated.pdb
        parmfile system_solvated.prmtop
        amber on
        exclude scaled1-4
        1-4scaling 0.83333
        rigidBonds all
        readexclusions yes
        scnb 2.0
        watermodel tip4p
        minimization on
        numsteps 5000

And if I launch this, it'll issue the error :
FATAL ERROR: Hydrogen group error caught in rattle1().

I found this in the namd mailing list :
but I checked in the FF definitions from amber and found that there was actually a force constant defined for this bond, so I do not have any further ideas on how to solve this problem.

Any idea would be of great help.

Thank you in advance

Peter Schmidtke, PhD

Scientific Project Manager

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Received on Fri Jul 24 2015 - 01:30:03 PDT
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