Dear amber developers,
Because I am still a little confused, I show the input file below. Hoping to get your advice.
.GENERAL
VERBOSE 0
PARALLEL 0
#
PREFIX snapshots
PATH ../01_extract_snapshots/
START 1
STOP 591
OFFSET 10
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../pbsa_com_prmtop
RECPT ../pbsa_rec_prmtop
LIGPT ../pbsa_lig_prmtop
#
GC 0
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 1
################################################################################
.NM
PROC 1
#
MAXCYC 10000
DRMS 0.05
#
IGB 1
SALTCON 0.0100733
EXTDIEL 80.0
SURFTEN 0.0072
DIELC 1
################################################################################
.PROGRAMS
note: the MD simulation ran under condition NVT.
Thanks.
Qiankun
> -----原始邮件-----
> 发件人: "David A Case" <david.case.rutgers.edu>
> 发送时间: 2018-09-12 10:21:37 (星期三)
> 收件人: "龚乾坤" <m201770109.hust.edu.cn>
> 抄送: I hope to get your advice
> 主题: Re: Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL
>
> On Wed, Sep 12, 2018, 龚乾坤 wrote:
>
> > The following is nmode_lig.181.out file. The file suggests that the
> > finally RMS is 0.078, which is large than 0.05(Convergence criterion
> > for the energy gradient),
> > and the calculation stoped. I want to know how to deal with this
> > problem, and run calculation once (the calculation process does not
> > stop).
> >
> > MIN: Iter = 980 NFunc = 8239 E = -2769.57629 RMSG = 7.8141459e-02
> > MIN: Iter = 981 NFunc = 8248 E = -2769.57629 RMSG = 7.8141459e-02
>
> ...
>
> > MIN: Iter = 1000 NFunc = 8419 E = -2769.57629 RMSG = 7.8141459e-02
>
> You clearly got completely "stuck" in the minimization, and it stopped
> after 1000 iterations. You should look at what sort of minimization you
> are carrying out, and whether or not SHAKE is turned on.
>
> There is a sample minimization/normal mode script in
> AMBERHOME/AmberTools/benchmarks/nab/bench_nm.nab. See what happens if
> you adapt that to your problem. Generally, though, xmin minimization
> should not get stuck in the way you see. It's hard to say more without
> knowing the nature of the system you are looking at, or anything about
> what minimization options you have used. But you should try to get the
> RMS gradient below 10^-6 or so, before proceeding to normal modes.
>
> ....dac
>
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Received on Wed Sep 12 2018 - 00:30:01 PDT
