Professor Case,
Thank you for the advise. I followed the tutorial of thermodynamic
integration using xleap.
I generated phe_coul.off, prmtop.coul.vac and prmcrd.coul.vac files as
instructed.
I also created a prmtop file without the perturbation such as
saveAmberParm PHE prmtop_wo_perturb.vac
since to minimize, heat and equilibrate the prmcrd.coul.vac file I
needed
the prmtop file without the perturbation.
Then, when I run sander, I did not get DV/DL printout along with energy
component terms as shown in the tutorial. I am wondering what I have
done wrong.
Thank you very much.
My input file is:
&cntrl
ntr=0,
nstlim =1000, nscm=5, ntave=1000,
ntx=5, irest=1, ntb=0, ntpr=200,
dt=0.001, nrespa=2,
ntt=1, temp0 = 300., tautp=2.0,
ntc=2, ntf=2, tol=0.000001,
ntwr = 200, ntwx=50,
icfe=1, clambda=0.5,
cut=30.0,
/
Here is my sander output file:
------------------------------------------------------------------------
-------
1. RESOURCE USE:
------------------------------------------------------------------------
--------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
|Largest sphere to fit in unit cell has radius = 31.741
| New format PARM file being parsed.
| Version = 1.000 Date = 07/27/06 Time = 16:49:34
NATOM = 15 NTYPES = 4 NBONH = 8 MBONA = 7
NTHETH = 16 MTHETA = 8 NPHIH = 27 MPHIA = 9
NHPARM = 0 NPARM = 0 NNB = 68 NRES = 1
NBONA = 7 NTHETA = 8 NPHIA = 9 NUMBND = 4
NUMANG = 5 NPTRA = 3 NATYP = 4 NPHB = 0
IFBOX = 0 NMXRS = 15 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2216
| Hollerith 93
| Integer 516639
| Max Pairs 105
| Max Rstack 50195
| Max Istack 75
| Total 2428 kbytes
Running a free energy calculation with lambda = 0.500
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
------------------------------------------------------------------------
--------
2. CONTROL DATA FOR THE RUN
------------------------------------------------------------------------
--------
PHE
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 200, ntrx = 1, ntwr =
200
iwrap = 0, ntwx = 50, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 0, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 1000, nscm = 5, nrespa = 2
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
Free energy options:
klambda = 1
clambda = 0.50000
------------------------------------------------------------------------
--------
3. ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------------------
--------
PHE
begin time read from input coords = 20.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.05315400
------------------------------------------------------------------------
--------
4. RESULTS
------------------------------------------------------------------------
--------
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 39
| TOTAL SIZE OF NONBOND LIST = 39
Etc....etc and then
NSTEP = 400 TIME(PS) = 20.400 TEMP(K) = 281.37 PRESS =
0.0
Etot = 25.6971 EKtot = 8.6666 EPtot =
17.0306
BOND = 3.3727 ANGLE = 5.0018 DIHED =
4.7470
1-4 NB = 3.5226 1-4 EEL = -0.9908 VDWAALS =
-0.0899
EELEC = 1.4673 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------
------
NSTEP = 1000 TIME(PS) = 21.000 TEMP(K) = 312.41 PRESS =
0.0
Etot = 25.2600 EKtot = 9.6228 EPtot =
15.6372
BOND = 4.1250 ANGLE = 3.8493 DIHED =
3.7038
1-4 NB = 3.8120 1-4 EEL = -1.0806 VDWAALS =
-0.2468
EELEC = 1.4745 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------
------
|=======================================================================
========
A V E R A G E S O V E R 500 S T E P S
NSTEP = 1000 TIME(PS) = 21.000 TEMP(K) = 347.88 PRESS =
0.0
Etot = 25.5975 EKtot = 10.7152 EPtot =
14.8823
BOND = 2.6576 ANGLE = 4.8593 DIHED =
3.3766
1-4 NB = 3.8354 1-4 EEL = -1.0028 VDWAALS =
-0.2805
EELEC = 1.4367 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------
------
R M S F L U C T U A T I O N S
NSTEP = 1000 TIME(PS) = 21.000 TEMP(K) = 55.15 PRESS =
0.0
Etot = 0.2170 EKtot = 1.6986 EPtot =
1.7270
BOND = 1.1283 ANGLE = 1.3492 DIHED =
1.2453
1-4 NB = 0.3651 1-4 EEL = 0.0708 VDWAALS =
0.0902
EELEC = 0.0508 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------
------
DV/DL, AVERAGES OVER 500 STEPS
NSTEP = 1000 TIME(PS) = 21.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------
------
|=======================================================================
========
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of David A. Case
Sent: Wednesday, July 26, 2006 12:45 PM
To: amber.scripps.edu
Subject: Re: AMBER: how to mutate in amber 8 for thermodynamic
integration without using xleap. .
On Tue, Jul 25, 2006, Lwin, ThuZar wrote:
>
> I am learning how to do thermodynamic integration using amber8. I
would
> like to mutate Alanine to Glycine by mutating the side chain CH3 to H.
> Here is what I did in tleap. Please let me know what I am doing
wrong.
>
> a = sequence{ALA}
> set a.CB pertName HA3
The syntax is unit-name.residue.atom-name, e.g. "a.1.CB", not "a.CB".
However, I really recommend that you use xleap, visually select all
atoms
in your structure, and use the "edit selected atoms" command. That will
give you a spreadsheet that shows which things need to be modified.
And, if you are thinking long-range, it would be good to update to Amber
9,
since the way in which thermodynamic integration is implemented is quite
different there.
...regards...dac
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Received on Sun Jul 30 2006 - 06:07:11 PDT
