AMBER Archive (2009)

Subject: Re: [AMBER] MMGBSA error

From: Jason Swails (jason.swails_at_gmail.com)
Date: Fri Dec 25 2009 - 07:28:15 CST


Hello,

It would appear the only reason there's a "virtual box" needed for the
minimization is that it's using ewald... I'm not sure why an ewald
parameter is set, since nmode is calculating gas phase vibrational
entropies anyway. Perhaps removing the &ewald namelist in the
minimization input will fix your problems...

Others may correct me if this is essential for the minimization in
this case, but it doesn't seem necessary for the minimization. If you
can find in the code where this part of the mdin is written, you may
be able to turn it off.

Good luck!
Jason

2009/12/25 Zhongjie Liang <zjliang_at_mail.shcnc.ac.cn>:
> Dear usersúČ
>
> I got 100 snapshots from the trajectory file. My input parameter file was
> as follows:
>
>
>
> @GENERAL
>
> PREFIX snaps
>
> PATH ./
>
> COMPLEX 1
>
> RECEPTOR 1
>
> LIGAND 1
>
> COMPT ./complex.top
>
> RECPT ./protein.top
>
> LIGPT ./lig.top
>
> GC 0
>
> AS 0
>
> DC 0
>
> MM 1
>
> GB 1
>
> PB 0
>
> MS 0
>
> NM 1
>
> @MM
>
> DIELC 1.0
>
> @GB
>
> IGB 2
>
> GBSA 1
>
> SALTCON 0.00
>
> EXTDIEL 80.0
>
> INTDIEL 1.0
>
> SURFTEN 0.0072
>
> SURFOFF 0.00
>
> @NM
>
> DIELC 4
>
> MAXCYC 10000
>
> DRMS 0.01
>
>
>
> And the sanmin_com.in file generated by mmpbsa.pl was as follows:
>
>
>
> &cntrl
>
> ntxo = 0,
>
> ntf = 1, ntb = 0,
>
> dielc = 4,
>
> cut = 99.0, nsnb = 99999,
>
> scnb = 2.0, scee = 1.2,
>
> imin = 1, maxcyc = 10000,
>
> ncyc = 0, drms = 0.01
>
> &end
>
> &ewald
>
> eedmeth= 5,
>
> &end
>
>
>
> I know it would calculate the free energy of each structure one by one. When
> it was doing the minimization of complex 26, it stopped and the error
> message in the sanmin_com.26.out was as follow:
>
>
>
> The system has extended beyond
>
> the extent of the virtual box.
>
> Restarting sander will recalculate
>
> a new virtual box with 30 Angstroms
>
> extra on each side, if there is a
>
> restart file for this configuration.
>
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
>
> Atom out of bounds. If a restart has been written,
>
> restarting should resolve the error
>
>
>
> I don't understand the principle of the MM/GBSA quite well, but it seems
> that it used the virtual box in the calculation.
>
> How to deal with the problem except removing the 26 structures. Any
> suggestion would be appreciated.
>
>
>
> Zhongjie Liang
>
> zjliang_at_mail.shcnc.ac.cn
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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