From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Mon Nov 05 2007 - 08:09:45 CST
Hi, Shulin,
You can check the structure you are simulating first by looking at it
in VMD. You need to load the psf file and then the pdb file to see
whether there are atoms bonded incorrectly because of the deletion of
the last residue.
Hope this will help.
Best,
Long
Quoting Shulin Zhuang <shulin.zhuang_at_gmail.com>:
> Hi, too sorry to send the third email to disturb you.
>
> When the 89 residue is deleted, the 88 residue Glu becomes the last residue,
> when I use autopsf to generate the psf and use CTER patch, I find that, the
> 88 Glu has 4 O atom, OT1, OT2, OE1 OE2. Should I not use the CTER patch or
> delete either OT1 or OT2.
>
> Too sorry to send you three email at one time. I am indeed very anxious
> about it.
>
> After CTER patch, this is the atom coordinates of last residue Glu 88:
>
> ATOM 1345 C GLU A 88 18.388 -5.329 2.808 1.00 0.00 P1
> C
> ATOM 1346 OT1 GLU A 88 18.435 -4.333 2.887 0.00 0.00 P1
> O
> ATOM 1347 OT2 GLU A 88 18.687 -6.170 3.258 0.00 0.00 P1
> O
> ATOM 1348 N GLU A 88 17.112 -4.455 0.869 1.00 0.00 P1
> N
> ATOM 1349 HN GLU A 88 17.679 -4.190 0.094 0.00 0.00 P1
> H
> ATOM 1350 CA GLU A 88 17.573 -5.692 1.563 1.00 0.00 P1
> C
> ATOM 1351 HA GLU A 88 16.731 -6.312 1.829 1.00 0.00 P1
> H
> ATOM 1352 CB GLU A 88 18.451 -6.415 0.541 1.00 0.00 P1
> C
> ATOM 1353 HB1 GLU A 88 18.972 -7.135 1.000 0.00 0.00 P1
> H
> ATOM 1354 HB2 GLU A 88 19.131 -5.707 0.089 1.00 0.00 P1
> H
> ATOM 1355 CG GLU A 88 17.571 -7.040 -0.542 1.00 0.00 P1
> C
> ATOM 1356 HG1 GLU A 88 17.136 -6.316 -1.077 0.00 0.00 P1
> H
> ATOM 1357 HG2 GLU A 88 16.810 -7.653 -0.078 1.00 0.00 P1
> H
> ATOM 1358 CD GLU A 88 18.432 -7.907 -1.463 1.00 0.00 P1
> C
> ATOM 1359 OE1 GLU A 88 19.030 -7.356 -2.372 1.00 0.00 P1
> O
> ATOM 1360 OE2 GLU A 88 18.480 -9.106 -1.242 1.00 0.00 P1
> O
>
>
> On 11/4/07, Shulin Zhuang <shulin.zhuang_at_gmail.com> wrote:
>>
>> Sorry to add some information, I use 6 Na+ to neutralize the protein
>> -water system, however, after minimizing the system, these 6 Na+ seems
>> forming bonds with the TIP3P water. I do not know how to tackle this
>> problem. Shoud I delete the water involving with Na+. before the MD
>>
>> On 11/4/07, Shulin Zhuang <shulin.zhuang_at_gmail.com> wrote:
>> >
>> > Dear All,
>> >
>> > I do equilibration MD simulation of protein in water sphere with NAMD2.6.
>> > The protein is I27, 89 resiudes,pdb 1tit. I have once sucessfully do 1 ns
>> > equilibration of I 27. However, when this time, I just delete the last
>> > residue 89, when I run equilibration at 392 ns, the MD stops and give the
>> > error information:FATAL ERROR: Bad global exclusion count! How
>> can I tackle
>> > this problem.
>> >
>> > Here, I put my configuration file of equilibration MD. Wish anyone will
>> > help me out of this problem. Great thanks. Following is the configuration
>> > file. For this configuration file, I just use it to do 1 ns
>> equlibration of
>> > I 27 without deleting residue 89.
>> >
>> >
>> > #############################################################
>> > ## Production run MD run ##
>> > ## in Water Sphere ##
>> > #############################################################
>> >
>> > #############################################################
>> > ## ADJUSTABLE PARAMETERS ##
>> > #############################################################
>> >
>> > # molecular system
>> > set MOL 1tit
>> > structure ${MOL}_sol_ionize.psf
>> >
>> > set outputname ${MOL}_prod
>> > set prod_restart ${MOL}_prod_restart
>> >
>> > # after heating system
>> > set inprot ${MOL}_heat
>> > coordinates ${inprot}.coor
>> > velocities ${inprot}.vel
>> > extendedSystem ${inprot}.xsc
>> >
>> > set temperature 300 ;# initial temperature
>> >
>> > # Continuing a job from the restart files
>> > if {0} {
>> > set inputname myinput
>> > binCoordinates $inputname.restart.coor
>> > binVelocities $inputname.restart.vel ;# remove the "temperature"
>> > entry if you use this!
>> > extendedSystem $inputname.xsc
>> > }
>> >
>> > firsttimestep 0
>> >
>> > #############################################################
>> > ## SIMULATION PARAMETERS ##
>> > #############################################################
>> >
>> > # Input
>> > paraTypeCharmm on
>> > parameters par_all27_prot_lipid_na.inp
>> >
>> > # Spherical boundary conditions
>> > sphericalBC on
>> > sphericalBCcenter -1.9094337225 0.573376715183 0.0411463677883
>> > sphericalBCr1 31.2752613824
>> > sphericalBCk1 10
>> > sphericalBCexp1 2
>> >
>> > # Force-Field Parameters
>> > exclude scaled1-4
>> > 1-4scaling 1.0
>> > cutoff 13.0
>> > switching on
>> > switchdist 10.0
>> > pairlistdist 14.5
>> >
>> >
>> > # Integrator Parameters
>> > timestep 1.0 ;# 1fs/step
>> > nonbondedFreq 2
>> > fullElectFrequency 4
>> > stepspercycle 20
>> >
>> > # Constant Temperature Control
>> > # A: for heating, use temperature reassignment
>> > if {0} {
>> > reassignFreq 500 ;# tuned to be suit 'natural' heating for system.
>> > reassignTemp 25 ;# to start from 0 Kelvin, else always lagging by
>> > 25K.
>> > reassignIncr 25
>> > reassignHold $temperature
>> > }
>> >
>> > # B: for heating, Temperature coupling via Langevin dynamics
>> > if {1} {
>> > langevin on ;# do langevin dynamics
>> > langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
>> > langevinTemp $temperature
>> > langevinHydrogen no ;# couple langevin bath to hydrogens
>> > }
>> >
>> > # Constant Pressure Control (variable volume)
>> > if {0} {
>> > useGroupPressure yes ;# needed for 2fs steps
>> > useFlexibleCell no ;# no for water box, yes for membrane
>> > useConstantArea no ;# no for water box, yes for membrane
>> > langevinPiston on
>> > langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>> > langevinPistonPeriod 100
>> > langevinPistonDecay 50
>> > langevinPistonTemp $temperature
>> > }
>> >
>> > # for saving restart file
>> > if {0} {
>> > restartname $prod_restart
>> > restartfreq 200 ;# 500steps = every 0.5ps
>> > restartsave yes
>> > binaryrestart yes ;# yes will preserves more accuracy.
>> > }
>> >
>> > # Output
>> > outputName $outputname
>> > dcdfreq 200
>> > xstFreq 200
>> > outputEnergies 100
>> > outputTiming 100
>> > binaryoutput yes
>> >
>> > # Fixed Atoms Constraint (set PDB beta-column to 1)
>> > if {0} {
>> > fixedAtoms on
>> > fixedAtomsForces on
>> > fixedAtomsFile fix_backbone.pdb
>> > fixedAtomsCol B
>> > }
>> >
>> > # IMD Settings (can view sim in VMD)
>> > if {0} {
>> > IMDon on
>> > IMDport 3000 ;# port number (enter it in VMD)
>> > IMDfreq 1 ;# send every 1 frame
>> > IMDwait no ;# wait for VMD to connect before running?
>> > }
>> >
>> > #############################################################
>> > ## EXTRA PARAMETERS ##
>> > #############################################################
>> >
>> > # Put here any custom parameters that are specific to
>> > # this job (e.g., SMD, TclForces, etc...)
>> >
>> > #constantforce yes
>> > #consforcefile ../common/example-output/ubq_ww_eq2.ref
>> >
>> > #############################################################
>> > ## EXECUTION SCRIPT ##
>> > #############################################################
>> >
>> > # Minimization
>> > if {0} {
>> > minimize 3000
>> > }
>> >
>> > run 1000000
>> > #production for 1ns
>> >
>> >
>> >
>> >
>> >
>>
>
-- Yinglong Miao Ph.D. Candidate Center for Cell and Virus Theory Chemistry Department, Indiana University 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405 1-812-856-0981(office); http://ylmiao.dict.cn/mypage/
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