Hi, Calos:
Thank you for offering me help. I would like to learn how to do it
using tgtfitmask. What I want to do is to drag a group of molecules in
"rna_3a_new_pull3.rst" to the location of those molecules in the reference
file "rna_3a_new_reference.inpcrd". Below is the code. Could you tell me
how to change it using tgtfitmask?
Thank you very much!
Li
cat>mdtgt_measure.in<<EOF
trajin ${protein}_pull3.rst
reference ${protein}_reference.inpcrd
rms reference
(:470,471,487&!.H=)|:498-499.P,OP1,OP2,O5',C5',O4',C4',O3',C3',C2',C1'
nofit out mdtgt_dist.dat
EOF
$AMBERHOME/bin/cpptraj -p ${protein}.prmtop<mdtgt_measure.in
set aa=`grep -v "#" mdtgt_dist.dat | awk '{print $2}'`
cat>mdtgt.in<<EOF
#regular vacuum md, backbone restrained
&cntrl
imin = 0, ntx = 1, nstlim = 50000, irest=0,
dt = 0.002, ntc = 2, ntf = 2,
temp0 = 50.0,
ntpr = 500, ntwx = 500, ntwr = 50000,
ntb = 1, ntt = 3, ntp=0,dielc=80.0,
nscm = 0, nmropt = 1,
ntr = 1, restraint_wt=50,
restraintmask=":1-94,163-469&!.H=",
itgtmd = 1, tgtrmsd = ${aa}, tgtmdfrc = 5,
tgtrmsmask="(:470,471,487&!.H=)|:498-499.P
,OP1,OP2,O5',C5',O4',C4',O3',C3',C2',C1'",
/
&wt
TYPE='TGTRMSD', istep1=1, istep2=25000,
value1 = ${aa}, value2 = 0.0,
/
&wt
TYPE='TGTRMSD', istep1=25000, istep2=50000,
value1 = 0.0, value2 = 0.0,
/
&wt
type="END",
/
EOF
$AMBERHOME/bin/sander -O -i mdtgt.in -o ${protein}_mdtgt.out -p
${protein}.prmtop -c ${protein}_pull3.rst -ref ${protein}_reference.inpcrd
-r ${protein}_mdtgt.rst -x ${protein}_mdtgt.mdcrd
On Fri, Apr 17, 2015 at 10:17 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> oh I see - you didn't define tgtfitmask. for most cases you probbly DO want
> best fit, so using nofit wouldn't make sense. I suggest removing the nofit,
> and then define the tgtfitmask in sander mdin. I could help more if I knew
> better what you want to do.
> carlos
>
> On Fri, Apr 17, 2015 at 1:10 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
>
> > HI. Calos:
> > Thank you for the reply. You are right, my initial rmsd is wrong
> since I
> > didn't turn nofit on when using cpptraj to measure it. It works normal
> now.
> >
> > Thank you very much!
> > Li
> >
> > On Fri, Apr 17, 2015 at 5:24 AM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > it will helpo us to check the files if you can explain exactly what
> > you're
> > > trying to do here. what is the initial structure, what is the reference
> > > structure, what do you intend? My guess is that your initial structure
> > and
> > > reference structure have rmsd values that don't match your input, but
> > > that's just a guess. maybe try running this with force constant of 0
> and
> > > ntpr=1 and see what your output tells you.
> > >
> > > On Fri, Apr 17, 2015 at 2:45 AM, 肖立 <xiaoli19871216.gmail.com> wrote:
> > >
> > > > Hi, all:
> > > >
> > > > I run targeted MD with the .in file shown as below,
> > > >
> > > > "
> > > >
> > > > #regular vacuum md, backbone restrained
> > > >
> > > > &cntrl
> > > >
> > > > imin = 0, ntx = 1, nstlim = 50000, irest=0,
> > > >
> > > > dt = 0.002, ntc = 2, ntf = 2,
> > > >
> > > > temp0 = 50.0,
> > > >
> > > > ntpr = 500, ntwx = 500, ntwr = 50000,
> > > >
> > > > ntb = 2, ntt = 3, ntp=1,
> > > >
> > > > nscm = 0, nmropt = 1,
> > > >
> > > > ntr = 1, restraint_wt=50,
> > > >
> > > > restraintmask=":1-94,163-469&!.H=",
> > > >
> > > > itgtmd = 1, tgtrmsd = 6.1919, tgtmdfrc = 5,
> > > >
> > > > tgtrmsmask="(:470,471,487&!.H=)|:498-499.P
> > > > ,OP1,OP2,O5',C5',O4',C4',O3',C3',C2',C1'",
> > > >
> > > > /
> > > >
> > > > &wt
> > > >
> > > > TYPE='TGTRMSD', istep1=1, istep2=25000,
> > > >
> > > > value1 = 6.1919, value2 = 0.0,
> > > >
> > > > /
> > > >
> > > > &wt
> > > >
> > > > TYPE='TGTRMSD', istep1=25000, istep2=50000,
> > > >
> > > > value1 = 0.0, value2 = 0.0,
> > > >
> > > > /
> > > >
> > > > &wt
> > > >
> > > > type="END",
> > > >
> > > > /
> > > >
> > > > "
> > > >
> > > >
> > > > However, it gives me the error as :
> > > >
> > > > "
> > > >
> > > > vlimit exceeded for step 48; vmax = 235.5863
> > > >
> > > >
> > > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > >
> > > > deviation is too large
> > > >
> > > > NITER, NIT, LL, I and J are : 0 0 3905 7743 7744
> > > >
> > > >
> > > > Note: This is usually a symptom of some deeper
> > > >
> > > > problem with the energetics of the system."
> > > >
> > > >
> > > > Could anyone tell me what's wrong with it and how to run it
> correctly?
> > > >
> > > >
> > > > Thank you very much!
> > > >
> > > > --
> > > > Li Xiao
> > > > University of California, Irvine
> > > > Email: xiaoli19871216.gmail.com
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Li Xiao
> > University of California, Irvine
> > Email: xiaoli19871216.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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>
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Fri Apr 17 2015 - 11:30:02 PDT
