Got it. When I chose "AMBER Coordinates with Periodic Box" this time in VMD, everything goes well. THX a lot!
X. Li
________________________________________
From: DEBOSTUTI GHOSHDASTIDAR [debostutighosh.gmail.com]
Sent: 07 November 2011 17:28
To: AMBER Mailing List
Subject: Re: [AMBER] Protein structure heating into a mess
on vmd i mean
On Mon, Nov 7, 2011 at 10:57 PM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> What did you use to view? If you have used amber cordinates option then u
> have to use amber coordinates with periodic box option to view
>
> On Mon, Nov 7, 2011 at 10:48 PM, Xiaozhou Li <xli12.qub.ac.uk> wrote:
>
>> Dear AMBER users,
>>
>> I was trying to equilibrate the protein system as well as the cubic water
>> box surrounded but something unexpected happened.
>>
>> When equilibration (after minimization) started the structure suddenly
>> went into a mess (refer to the image attached to this mail).
>>
>> BTW, when I shifted "ntb=1" into "ntb=0" in the heating step, the
>> structure was well. I'm wondering that is there anything wrong with the
>> periodic boundary condition? Plus, I've checked structures generated by
>> minimization steps and they are all right.
>>
>> Below are scripts which I utilized to generate the solvent box, add
>> sodium ions, saving parameter and topology files and did minimization works.
>>
>> -----------------------------------------------------------------------
>> > tleap
>> > source leaprc.gaff
>> > source leaprc.ff99SB
>> > source leaprc.ff10
>> > comp = loadpdb structure.pdb
>> > solvatebox comp TIP3PBOX 8.0
>> > addions comp Na+ 0
>> > saveoff comp structure.off
>> > loadamberparams frcmod.ionsjc_spce
>> > saveamberparm comp structure_wb.prmtop structure_wb.inpcrd
>> -----------------------------------------------------------------------
>> Initial minimization ------water
>> &cntrl
>> imin=1,
>> maxcyc=5000,
>> ncyc=2500,
>> ntwx=100,
>> ntb=1,
>> ntr=1,
>> cut=10.0,
>> restraint_wt=5.0,
>> restraintmask=':1-396'
>> /
>> -----------------------------------------------------------------------
>> Initial minimization ------all
>> &cntrl
>> imin=1,
>> maxcyc=2500,
>> ncyc=1250,
>> ntwx=100,
>> ntb=1,
>> ntr=0,
>> cut=10.0
>> /
>> -----------------------------------------------------------------------
>> Heating - solvent and ions
>> &cntrl
>> imin=0,irest=0,ntx=1,
>> ntb=1,cut=10.0,
>> ntr=1,
>> restraint_wt=0.5,
>> restraintmask=':1-396',
>> ntc=2,ntf=2,
>> tempi=0.0,temp0=300.0,ntt=3,gamma_ln=1.0,
>> nstlim=20000,dt=0.001,
>> ntpr=100,ntwx=100,ntwr=200
>> /
>> -----------------------------------------------------------------------
>>
>> I'm quite appreciate if anybody could give me a hand.
>>
>> Many thanks,
>> X. Li
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Debostuti Ghosh Dastidar
> PhD Scholar
> Computational Biophysics Lab
> Department of Biotechnology
> Indian Institute of Technology Madras
>
--
Debostuti Ghosh Dastidar
PhD Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Mon Nov 07 2011 - 10:00:03 PST
