Dear amber users,
I finally found the problem. My system.pdb contained a few water molecules with residue name HOH (and not T4E), they were read by tleap but no lone pair was added. Renaming these to T4E did the trick.
Sorry for any disturbance.
Peter Schmidtke
-----Message d'origine-----
De : peter.schmidtke.discngine.servier.com [mailto:peter.schmidtke.discngine.servier.com]
Envoyé : vendredi 24 juillet 2015 10:28
À : amber.ambermd.org
Objet : [AMBER] Using TIP4PEW amber FF in NAMD
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
WAT=T4E
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):
NAMD :
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 :
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/4106.html
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
Discngine
Paris
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Received on Fri Jul 24 2015 - 05:30:03 PDT
