Dear AMBER users,
I am new to the AMBER simulation package. I want to simulate my system with
the TIP4PEW water model. I used the following tleap script:
********************************************
source leaprc.ff14SB
WAT=T4E
loadamberparams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew
loadamberparams frcmod.ionslrcm_cm_tip4pew
verbosity 2
********************************************************
I am using AmberTools15 for tleap and Amber12 for simulation. Surprisingly
I got the followings:
1. > loadamberparams frcmod.tip4pew
Loading parameters:
/home/applications/ambertools15/dat/leap/parm/frcmod.tip4pew
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP4P
*(UNKNOWN ATOM TYPE: EP)*
2. Loading parameters:
/home/applications/ambertools15/dat/leap/parm/frcmod.ionslrcm_cm_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Divalent ion parameters(CM set) for Particle Mesh Ewald and TIP4P/EW water
model from Li, Roberts, Chakravorty and Merz (JCTC 2013, 9, 2733-2748)
(UNKNOWN ATOM TYPE: Be2+)
(UNKNOWN ATOM TYPE: Cu2+)
(UNKNOWN ATOM TYPE: Ni2+)
(UNKNOWN ATOM TYPE: Pt2+)
(UNKNOWN ATOM TYPE: Zn2+)
................................
I have checked the leaprc file and the EP is defined. I dd also checked the
prmtop file by xparmed.py. Using the "print details" utility of xparmed.py
I got following information about water:
******************************************
ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass
Charge GB Radius GB Screen
159 10 WAT O OW 1.7759 0.1628 16.0000
0.0000 1.5000 0.8500
160 10 WAT H1 HW 0.0000 0.0000 1.0080
0.5242 0.8000 0.8500
161 10 WAT H2 HW 0.0000 0.0000 1.0080
0.5242 0.8000 0.8500
162 10 WAT EPW EP 0.0000 0.0000 0.0000
-1.0484 1.5000 0.8000
*******************************************
It seems that the parameter for EP is there in prmtop.
I am not able to understand why does then tleap says that EP is an unknown
atom type??
Looking forward for your reply.
Regards
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Received on Sat Dec 17 2016 - 04:00:02 PST
