Hi all,
i am using antechamber and creating parameter and coordinate files for 1IMX
for creating mol2 file i give the following command
antechamber -i sustiva_new.pdb -fi pdb -o
sustiva.mol2 -fo mol2 -c bcc -s 2
i am using antechamber and creating parameter and coordinate files for 1IMX
for creating mol2 file i give the following command i rename my insulin protein 1IMX with sustiva after that when i run this command it generate an error
/Desktop/Softwares/amber14/bin/1mx$ antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
Running: /home/comsats/Desktop/Softwares/amber14//bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /home/comsats/Desktop/Softwares/amber14//bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 468; net charge: 0
Running: /home/comsats/Desktop/Softwares/amber14//bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/comsats/Desktop/Softwares/amber14//bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
and sqm.out file showing error:
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.3142E+07 DeltaE = -0.2242E-09 DeltaP = 0.4663E-13
QMMM: Smallest DeltaE = 0.1869E-09 DeltaP = 0.2397E-06 Step = 3
how can i resolve this error please guide me and also guide me why this error occur.
From: ayesha_comsian.hotmail.com
To: amber.ambermd.org
Subject: RE: [AMBER] query for plotting enthalpy graph
Date: Sat, 14 Nov 2015 19:09:26 +0500
Dear Jason M. Swails,
i am attaching a paper, in which author plotted graph for Enthalpy's and Entropy's fluctuations and the accumulated mean values. I exactly want to plot graph like that please take a look on this paper. i could not under stand how can he plot it. and what i have to need for plotting it.
> From: jason.swails.gmail.com
> Date: Sat, 14 Nov 2015 08:58:23 -0500
> To: amber.ambermd.org; ayesha_comsian.hotmail.com
> Subject: Re: [AMBER] query for plotting enthalpy graph
>
> Please check your spam folder. I already answered this question on the mailing list a few hours ago.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> > On Nov 14, 2015, at 8:53 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com> wrote:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Hi all,
> >
> > i
> > want to know if i want to plot graph for enthalpy how is it possible
> > ?
> >
> > because in Amber advanced tutorial when i used given mdcrd
> > file it only generates one value for Delta G.
> >
> > i put the
> > following inputs for mmbsa.in
> >
> > is it possible if i use 1000
> > frames then MMPBSA.py also calculate 1000 binding energies ? how can
> > i plot graph for it please guide me.
> > Input file for running PB and GB
> > &general
> > endframe=50, verbose=1,
> > # entropy=1,
> > /
> > &gb
> > igb=2, saltcon=0.100
> > /
> > &pb
> > istrng=0.100,
> > /
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 20 2015 - 00:00:04 PST
