AMBER Archive (2002)

Subject: Re: nonpeoridic boundary + mm/gbsa

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Mon Nov 11 2002 - 10:59:27 CST

Hi,

did you have a look at one of the snapshots which give strange energies?
Make a pdb file out of the crd file and see how the molecule looks like.
My guess is that your coordinates do not fit your parmtop file, hence
the large internal energies. Check NTOTAL, LSTART/LSTOP, RSTART/RSTOP in
mm_pbsa.in again.

Best regards

Holger

> 3) 50 snapshots from 200-ps were selected excluding the Cl- and water.
> MM-gbsa is used for free energy analyse, but the results for "mm" are
> wrong. for examples. the output flie of complex: md0_com.all.out
>
> -----------------------------------------------------------------------------------
> 1
> BOND = 740.7613 ANGLE = 2306.6874 DIHED = 1846.5806
> VDWAALS = -2197.5598 EEL = -22133.2883 EGB = -2799.7455
> 1-4 VDW = 1116.9826 1-4 EEL = 12097.1717 RESTRAINT = 0.0000
> surface area = 11772.7024
> 2
> BOND = 8963956.6611 ANGLE = 434657.9063 DIHED = 14200.9224
> VDWAALS = ************* EEL = -8219.6179 EGB = -9826.2583
> 1-4 VDW = ************* 1-4 EEL = 121.2314 RESTRAINT = 0.0000
> surface area = 10079.3468
> 3
> BOND = 12112917.0404 ANGLE = 416392.2410 DIHED = 14458.5766
> VDWAALS = ************* EEL = -9529.6581 EGB = -9079.9973
> 1-4 VDW = ************* 1-4 EEL = 1506.4992 RESTRAINT = 0.0000
> surface area = 9999.9357
> 4
> BOND = 14752382.6272 ANGLE = 403583.8930 DIHED = 13299.6043
> VDWAALS = 17681778.7122 EEL = -7882.3246 EGB = -9762.7571
> 1-4 VDW = 6543237.0117 1-4 EEL = 528.1584 RESTRAINT = 0.0000
> surface area = 9481.7892
> ---------------------------------------------------------------------------------
> the input file for "MM" analyse
> ------------------------------------------------------------------------------
> File generated by mm_pbsa.pl. Using MM GB MS
>
> &cntrl
> ntf = 1, ntb = 0, dielc = 1, idecomp= 0, igb = 1, saltcon= 0.0,
> offset = 0.09, extdiel= 80.0, gbsa = 1, surften= 1.0, cut = 99999.0,
> nsnb = 99999, scnb = 2.0, scee = 1.2, imin = 1, maxcyc = 1,
> ncyc = 0,
> &end
> ---------------------------------------------------------------------------------
>
> How could I do? Thank you in advance.
> 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++