AMBER Archive (2007)

Subject: AMBER: Input files for the Potential of mean force.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Sun Jun 10 2007 - 21:43:12 CDT

Thank you Carlos.

It is the input file that I used. I firstly fix the position of the
receptor active site by position restraint as folllows:

Production MD
&cntrl
  imin=0, saltcon=0.5
  nstlim=5000, dt=0.002, ntc=1, ntr=1, nmropt=1
  ntpr=100, ntwx=100,
  cut=16, ntb=0, igb=1,
  ntt=3, gamma_ln=1.0,
  tempi=300.0, temp0=300.0,
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=1.restraint
DUMPAVE=1_md1.result
Keep upper residues 1 2 3 4 fixed with weak restraints
10.0
RES 1 2 3 4
END
END

Then, In order to monitor the PMF along 1D axis, defined as the distance
between residue 4_at_P (represent the receptor), and residue 5_at_O18 (represent
the drug). Then, I change the distance restraint from 1 to 40A. But at
the same time, I think I should keep the drug at the same orientation
relative to the receptor, I fixed the angle restraint at 0 degree for all
the umbrella sampling runs. Here is one of the restraint file I used.

# variable distance restrainst
&rst iat=4,5 r1=0.0, r2=20.0, r3=20.0, r4=100.0, rk2 = 100.0, rk3 = 100.,
iresid=1,
ATNAM(1)=P,
ATNAM(2)=O18/

# fixed angle restraint
&rst iat=4,5,5,5 r1=0.0, r2=0.0, r3=0.0, r4=360.0, rk2 = 1000.0, rk3 =
1000.0, iresid=1,
ATNAM(1)=P,
ATNAM(2)=N10,
ATNAM(3)=N12,
ATNAM(4)=O18/

Then, I run the production MD as follows:
$AMBERHOME/exe/sander -O -i 1_md1.in -o 1_md1.out -c 1_min.rst -p 1.prmtop
-r 1.md1.rst -x 1_md1.mdcrd -ref 1_min.rst

However, the 1.results that I got is as follows:
................
     150 20.475 -107.033
     160 21.152 25.018
     170 21.537 -159.681
     180 22.024 -15.385
     190 25.157 48.197
     200 26.163 -95.016
     210 18.122 -8.224
     220 16.849 -161.385
     230 16.536 50.669
     240 18.476 -65.738
     250 21.368 19.429
     260 20.551 149.414
     270 18.940 -76.680
     280 21.190 107.498
     290 22.064 105.608
     300 21.552 18.125
     310 20.152 -35.505
     320 23.703 -103.914
     330 20.593 24.769
     340 21.915 -13.790
     350 26.825 119.012
     360 20.678 25.467
     370 24.278 70.666
     380 19.640 -92.523
.................

I noticed the angle was changing in this umbrella sampling run. Should I
try to fix the relative orientation of the drug and receptor for a PMF
calculation? If yes, what should I do to fix the angle? Did I do anything
wrong here? Thanks!

Best regards,

Cat.

>From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: Potential of mean force.
>Date: Fri, 8 Jun 2007 08:08:06 -0400
>
>you should probably send your corrected restraint input file if you
>want us to check it.
>
>On 6/8/07, Catein Catherine <askamber23_at_hotmail.com> wrote:
>>
>>Dear Jerome and other PMF experists,
>>
>>Thank you very much! I did the calculations.
>>
>>I did the PMF calculations accordingly, however, when I tried to do the
>>PMF
>>along a distance form 1 to 40 A), but keeping the angle unchanged with the
>>corrected input files below. As I want the drug move away from the
>>receptor
>>along a 1-D axis, I did a series of umbrella sampling MD runs with the
>>following restrainst.
>>
>>Angle Distance
>>-----------------------------------
>>180.0 1.0
>>180.0 2.0
>>180.0 3.0
>>180.0 4.0
>>.......
>>......
>>180.0 40.0
>>
>>While the distances were changing from 1.0 to 40.0A as expected, the angle
>>also changed from 120.0 to 230.0, even I keep using the same restaint at
>>180.0 for all the umbrella sampling MD runs.
>>
>>Is it just normal?
>>
>>Can I still use the distance histogram for the PMF calculations but
>>ingoring
>>the changes in angles?
>>
>>Should I keep increasing the force constant for the angle restraint untill
>>the angle don't vary at all?
>>
>>Please kindly share your experiences with me.
>>
>>Thanks
>>
>>Cat
>>
>>
>> >From: Jerome.GOLEBIOWSKI_at_unice.fr
>> >Reply-To: amber_at_scripps.edu
>> >To: amber_at_scripps.edu
>> >Subject: Re: AMBER: How to fix two angle but do umberlla sampling
>> >fordistance?
>> >Date: Thu, 07 Jun 2007 17:38:26 +0200
>> >
>> >Hi,
>> >Your procedure seems OK, you can put various restaint in a simple rst
>> >file.
>> >However, in your restraint file, "iat" is supposed to correspond to the
>> >atom number in your pdb file.
>> >If you want to restraint the distance between the first 2 atoms of your
>> >structure, you should have :
>> >iat=1,2
>> >For an angle restraint you should have 3 atoms (ex iat=1,2,3) and 4 for
>> >a dihedral (iat=7,8,9,10)
>> >
>> > > # fixed angle restrainst
>> > >
>> > > &rst iat=4,5,5 r1=-180.0, r2=180.0, r3=180.0, r4=180.0, rk2 = 1000.0,
>> >rk3 =
>> > ^^^^^^^
>> >
>> >here I don't understand why you write 5,5
>> >
>> > > &rst iat=4,5,5,5 r1=0.0, r2=0.0, r3=0.0, r4=360.0, rk2 = 1000.0, rk3
>>=
>> > ^^^^^^
>> >
>> >look at your PDB and write the good atom numbers. There is no need to
>> >add additional inforamtion on the atom name (at least on AMBER 8.0,
>> >maybe it changed for A9, but I don't see why)
>> >
>> >Good lick
>> >Jerome
>> >--
>> >Jerome Golebiowski, PhD
>> >LCMBA, team Chemometrics and Molecular Modeling
>> >University of Nice, parc Valrose
>> >06108 Nice Cedex2 France
>> >tel : +33 (0)4 92 07 61 03
>> >http://www.unice.fr/lcmba
>> >http://www.unice.fr/lcmba/golebiowski
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