Dear Sir/Madam,
I am new to PMF type calculations, and i could like to perform a umbrella
sampling for a system like this. We are interest to monitor the process for
the drug to move at a specific direction from the receptor binding pocket,
like this:
RECEPTOR ______________
BINDING | Drug------------> remove from this direction only
POCKET _______________
I tried to set the distance restraint for a simiplied systems with RESIDUE
1to 4 as the receptor binding pocket, and residue 5 as the drug, and do the
calculation as follows:
(1) keeping the receptor binding pocket (RESIDUES 1,2,3,4) fixed
(2) Increase the distance of the drug (RESIDUE 5, center of mass) from an
atom in receptor
However, I noted that the drug is in fact moving in more than one direction,
and the drug catch with the receptor binding pocket. Here is my input
files, could you please kindly help me to point out what did I did wrong?
-------------------------------------MY INPUT
FILE--------------------------------------------------
Umbrella sampling MD
&cntrl
imin=0, irest=1, ntx=5, saltcon=0.4
nstlim=3000, 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=residue.restraint
DUMPAVE=residue.result
Keep upper residues 1 2 3 4 fixed with weak restraints
10.0
RES 1 4
END
END
=========================MY residue.restraint
FILE==================================
# distance restrainst for drug
&rst iat=4,5, r1=10.0, r2=13.0, r3=15.0, r4=20.0, rk2 =30.0, rk3 = 30.,
iresid=1, ir6=0,
ATNAM(1)=P,
ATNAM(2)=C31,ATNAM(2)=C25,ATNAM(2)=C21,ATNAM(2)=C16,ATNAM(2)=C8,ATNAM(2)=O24,ATNAM(2)=C20,ATNAM(2)=O23,ATNAM(2)=O22,ATNAM(2)=C19,ATNAM(2)=C15,ATNAM(2)=C14,ATNAM(2)=O18,ATNAM(2)=N12,ATNAM(2)=C11,ATNAM(2)=C10,ATNAM(2)=C13,ATNAM(2)=C9,ATNAM(2)=N10,ATNAM(2)=C5,ATNAM(2)=C4,ATNAM(2)=C3,ATNAM(2)=C,ATNAM(2)=O,ATNAM(2)=C2,ATNAM(2)=C1,ATNAM(2)=C6,ATNAM(2)=C7,ATNAM(2)=C17,ATNAM(2)=C98
/
===============================My OUTPUT FILE
==================================
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 62.200 TEMP(K) = 1651.00 PRESS =
0.0
Etot = 1193.3862 EKtot = 861.2264 EPtot =
332.1598
BOND = 183.2061 ANGLE = 291.2733 DIHED =
131.1998
1-4 NB = 68.9142 1-4 EEL = -381.9480 VDWAALS =
-22.4709
EELEC = -139.7952 EGB = -302.3838 RESTRAINT =
504.1644
EAMBER (non-restraint) = -172.0047
------------------------------------------------------------------------------
NMR restraints: Bond = 0.140 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 130 ; vmax = 23.8542427527606
vlimit exceeded for step 172 ; vmax = 49.3584438745089
NSTEP = 200 TIME(PS) = 62.400 TEMP(K) = 2084.33 PRESS =
0.0
Etot = 1538.8958 EKtot = 1087.2641 EPtot =
451.6318
BOND = 307.2185 ANGLE = 388.1555 DIHED =
130.5633
1-4 NB = 65.1899 1-4 EEL = -399.4312 VDWAALS =
-48.0505
EELEC = -111.9660 EGB = -312.9043 RESTRAINT =
432.8567
EAMBER (non-restraint) = 18.7751
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 204 ; vmax = 27.5963598323955
vlimit exceeded for step 209 ; vmax = 50.1837334599151
vlimit exceeded for step 210 ; vmax = 27.0051722625023
vlimit exceeded for step 213 ; vmax = 25.4720474595900
....
....
....
===============================================================================
NSTEP = 1600 TIME(PS) = 65.200 TEMP(K) =********* PRESS =
0.0
Etot = NaN EKtot = 955696.3416 EPtot = NaN
BOND = 179061.9638 ANGLE = 13542.3571 DIHED =
778.8009
1-4 NB = 25462.5365 1-4 EEL = -395.0060 VDWAALS =
5476.7559
EELEC = -101.9259 EGB = NaN RESTRAINT =
**************
EAMBER (non-restraint) = NaN
------------------------------------------------------------------------------
NMR restraints: Bond = 0.022 Angle = 0.000 Torsion = 0.000
=======================MY residue.result FILE ========================
0 11.869
10 12.228
20 12.772
30 12.905
40 12.841
50 12.837
60 13.088
70 13.198
80 13.075
90 12.799
100 12.946
110 13.168
120 13.350
130 13.455
140 13.397
150 13.396
160 13.242
170 13.005
180 12.694
190 12.779
200 13.053
210 13.073
220 13.142
230 13.191
240 13.181
250 13.453
260 13.560
270 13.554
....
....
....
470 15.027
480 15.027
490 15.027
500 15.027
510 15.027
520 15.027
530 15.027
540 15.027
550 15.027
560 15.027
570 15.027
580 15.027
590 15.027
600 15.027
610 15.027
620 15.027
630 15.027
640 15.027
650 15.027
660 15.027
670 15.027
680 15.027
690 15.027
... same till the end of the file
=============================================================
Cat
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Received on Sun May 13 2007 - 06:07:20 PDT
