[AMBER] Water do not see the system....

From: Vito GENNA <vito.genna.irbbarcelona.org>
Date: Wed, 10 Oct 2018 18:18:40 +0200

Dear all,

I decided to write here cause I am fresh to amber.
I have a big problem regarding solvation. Here the tleap input file I use:

*tleap Amber16*

*source leaprc.protein.ff14SBsource leaprc.water.tip3ploadamberparams
../../parms/MG.frcmodloadamberprep ../../parms/MG2.prepcomplex = loadpdb
protein2.pdb#setBox complex vdwsolvatebox complex TIP3PBOX 12addions
complex Cl- 0addions complex Na+ 0savepdb complex wprotein.pdbsaveamberparm
complex protein.prmtop protein.inpcrdsaveamberparm complex protein.top
Once i got the system I minimize it and what I note is that water molecules
dramatically overlap protein's atoms. The min.in input file attached:

*&cntrl imin=1, ntx=1, irest=0, maxcyc=1000, ncyc=1000, ntpr=100, ntwx=0,
cut=8.0, ntr = 1, restraint_wt = 25,
restraintmask = ':1-750' /*

Water behave as protein would not exist and, additionally, they get
dramatically close one to each other in an unphysical fashion.
Turning to the heating step, please see attached input file, the situation
become even more severe.

*&cntrl imin=0, irest=0, ntx=1, ntt=1, tempi=0.0, temp0=298.15,
tautp=1.0, ntb=1, ntc=2, ntf=2, cut=9.0, ntr=1, restraint_wt=50.0,
restraintmask=':1-750', nstlim=500000, dt=0.002, t=0.0, nscm=5000,
ntpr=500, ntwx=500, ntwe=0, ntwr=50000, ioutfm=1,/*

Now, the vdw energy does not change (does not even fluctuates around a
fixed value) and I guess that prorably I made some basic mistakes. Isn't it?
I tried with different wat models (tip3p and tip4p) as well as with
different amber versions (16 and 18) but result does not change.
Have you ever faced this problem? Is fo, what would be the cause and how
should I fix it?

Thanks in advance for any kind contribution.


*Vito Genna, Ph.D*
*EMBO Fellow*
*Postoctoral Researcher*
*Molecular Modeling and Bioinformatics*
*Orozco Lab*
*Institute for Research in Biomedicine (IRB Barcelona)*
*Parc Centific de Barcelona*
*C/ Baldiri Reixac 10-12*
*08028 Barcelona*
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Received on Wed Oct 10 2018 - 09:30:04 PDT
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