Dear Sir,
Many thanks for providing me a suitable suggestion to solve the error of
tleap for ligand (Anionic carboxylic acid).
Further, I want to simulate the same ligand
However, when I proceed for MD upto 250000 steps, the job stopped at 12000
steps in md.out file
Please kindly help me to solve the above mentioned error
The script for minimization as follows
&cntrl
imin=1,
ntx=1,
irest=0,
maxcyc=2000,
ncyc= 1000,
ntpr=100,
ntwx=0,
cut= 12.0,
/
END
The script for Heating and equilibrium step as follows
&cntrl
imin= 0,
irest=0,
NTX=1,
ntb= 1,
ntp=0,
NTPR=500,
NTWX=500,
Tempi=0.0,
Temp0=300.0,
NTT=3,
gamma_ln=2.0,
NTC=2,
NTF=2,
cut= 12.0,
nmropt=1,
ig=-1,
nstlim=10000,
dt=0.002,
/
&wt type='TEMP0', istep1=0, istep2=9000, value1=0.0, value2=300.0 /
&wt type='TEMP0', istep1=9001, istep2=10000, value1=300.0, value2=300.0 /
&wt type='END' /
~
The script for md step as follows
&cntrl
imin=0,
irest=1,
NTX=5,
ntb=2,
ntp=1,
PRES0=1.0,
TAUP=2.0,
NTPR=500,
NTWX=500,
NTWR=500,
Tempi=300.0,
Temp0=300.0,
NTT=3,
gamma_ln=2.0,
ig=-1,
NTC=2,
NTF=2,
cut=12.0,
nstlim=2500000,
dt=0.002
/
The script for job submission as follows
#!/bin/bash
#PBS -N Lig
#PBS -q gpu
#PBS -l nodes=1:ppn=1:gpus=1:exclusive_process
#PBS -l walltime=72:00:00
#PBS -V
#PBS -k oe
echo $CUDA_VISIBLE_DEVICES
export CUDA_VISIBLE_DEVICES=`cat $PBS_GPUFILE | awk -F"-gpu" '{ printf
A$2;A=","}'`
#REMEMBER TO CHANGE ME FOR WHATEVER DIRECTORY YOU ARE RUNNING IN
cd /cbio/jclab/projects/collab/suri/ramesh/dend15-4
#AMBER
export AMBERHOME=/cbio/jclab/projects/collab/amber14
#Run the minimization with just CPU AMBER.
$AMBERHOME/bin/pmemd -O -i Mini.in -o Mini.out -p LIG_solvated.top -c
LIG_solvated.crd -r Mini.rst -inf Min.mdinfo
#Run MD using GPU AMBER.
$AMBERHOME/bin/pmemd.cuda -O -i Heating.in -o Heating.out -p
LIG_solvated.top -c Mini.rst -r Heating.rst -x Heating.mdcrd -inf
Heating.mdifo
$AMBERHOME/bin/pmemd.cuda -O -i md.in -o md.out -p LIG_solvated.top -c
Heating.rst -r md.rst -x md.mdcrd -inf md.info
Thanks & regards
*Dr. Ramesh M*
Email: shreeramesh.gmail.com
Mobile: 91 + (0) 9646469938 27+ (0) 844556164
On Thu, Feb 5, 2015 at 1:23 AM, Marc van der Kamp <marcvanderkamp.gmail.com>
wrote:
> You need to load the frcmod file for the ions - the set that is compatible
> with the water model you use.
> So in your case, add the following to your leap-script:
>
> loadamberparams frcmod.ionsjc_tip3p
>
> --Marc
>
> On 5 February 2015 at 09:18, Shreeramesh <shreeramesh.gmail.com> wrote:
>
> > Dear All,
> >
> > I ran a tleap for the ligand, it is an anioc carboxylate molecule
> >
> > The script of tleap as follows. It includes Na+ ion to nuetralize the
> > carboxylate anion
> >
> > source leaprc.ff12SB
> > source leaprc.gaff
> > LIG = loadmol2 LIG.mol2
> > saveAmberParm LIG LIG.top LIG.crd
> > loadamberparams LIG.frcmod
> > check LIG
> > set default PBRadii mbondi2
> > saveAmberParm LIG LIG.top LIG.crd
> > charge LIG
> > addIons2 LIG Na+ 0
> > solvateBox LIG TIP3PBOX 10.0
> > saveAmberParm LIG LIG_solvated.top LIG_solvated.crd
> > savepdb LIG LIG_solvated.pdb
> > quit
> >
> >
> > I got the following error message and I request you to kindly help me to
> > solve it
> >
> > Error
> >
> > Building atom parameters.
> > For atom: .R<Na+ 2>.A<Na+ 1> Could not find vdW (or other) parameters for
> > type: Na+
> > For atom: .R<Na+ 3>.A<Na+ 1> Could not find vdW (or other) parameters for
> > type: Na+
> > Parameter file was not saved.
> >
> >
> > Please kindly suggest me a suitable source file for the counter ion like
> > Na+ or Cl- or Ag+ ion, etc.
> >
> >
> >
> >
> > Thanks & regards
> >
> > *Dr. Ramesh M*
> > Email: shreeramesh.gmail.com
> > Mobile: 91 + (0) 9646469938 27+ (0) 844556164
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
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Received on Fri Feb 06 2015 - 01:30:04 PST
