AMBER Archive (2008)

Subject: Re: AMBER: MM_PBSA problems in AMBER9

From: Ray Luo (rluo_at_uci.edu)
Date: Sun Oct 05 2008 - 22:20:01 CDT

The error message says that you should change fillratio NOT scale to a
larger number ...

All the best,
Ray

2008/10/5 欧阳德方 <ouyangdf1978_at_hotmail.com>:
>
> Hi, all,
>
> When I calculate the binding energy of RNA-small molecule interaction by MM_PBSA in AMBER9. Input file is as following:
>
> PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./den4_complex_major_vac.prmtop
> RECPT ./rna_vac.prmtop
> LIGPT ./dendrimer4.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 0
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> DIELC 1.0
> #
> #
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> #
> PROBE 0.0
> #
>
> But it shows "---snapshot_lig.crd.17 not successful---"
> The output file shows
> "---PB Bomb in setgrd (): focusing grid too large 2
> reset fillratio to a large number 2.000"
>
> According previous post, I change SCALE 2.0 to 4.0 (or 3.0). But new problems appears.
> The output file shows:
> "---
> WARNING: Missing PB for PB in 0 -> Taken from -1
> WARNING: Missing PB for PB in 1 -> Taken from 0
> WARNING: Missing PB for PB in 2 -> Taken from 1
> ---
> =>> Calc delta from raw data"
>
> Also the command lines shows:
> " ---
> Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
> Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
> No data for 0+2 PB PB 0"
>
> I cannot get the final statistical output file.
>
> Could u tell me the reasons and how to solve it?
>
> Thanks for your help,
>
> Ouyang
>
> School of Pharmacy
> The University of Queensland
> Brisbane, Australia
>
>
>
>
>
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