BY the way, here is the head of the script:
#!/bin/csh
set AMBERHOME=/home/lxiao/amber14
set LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:$AMBERHOME/lib
cd /home/lxiao/Paul_simulation/Paulsprotein/rna_3a
set protein='rna_3a_new'
Best,
Li
On Fri, Apr 17, 2015 at 11:03 AM, 肖立 <xiaoli19871216.gmail.com> wrote:
> 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
>
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Fri Apr 17 2015 - 11:30:03 PDT
