Dear chirag,
what is this?
sanjib.
On Wed, Jun 20, 2012 at 5:20 PM, <chirag740.gmail.com> wrote:
> A #44########################################Q
> ------Original Message------
> From: Sanjib Paul
> To: AMBER Mailing List
> ReplyTo: AMBER Mailing List
> Subject: [AMBER] problem during heating up the system
> Sent: Jun 20, 2012 15:43
>
> Dear Amber User,
> I am simulating HCAII using 2CBA.pdb. I am using
> CaDA approach. I have changed residue name as given in the paper
> "Novel Zinc Protein Molecular Dynamics Simulation: Steps Toward
> Antiangiogenesis for Cancer Treatment, Yuan-Ping Pang, J. Mol. Model.
> 1999,5,196-202," After minimisation I have heated up the system using
> following input file,
> heating of whole system
> &cntrl
> imin = 0,
> irest = 0,
> iwrap = 1,
> ntx = 1,
> ntb = 1,
> ntc = 2,
> ntf = 2,
> ntt = 3,
> ntr = 1,
> cut = 20.0,
> tempi = 0.0,
> temp0 = 300.0,
> gamma_ln = 1.0,
> nstlim = 25000,
> dt = 0.002,
> ntpr = 100,
> ntwx = 100,
> ntwr = 1000
> /
> Keep protein fixed with weak restraint
> 3.0
> RES 1 265
> END
> END
>
> But, I am getting a follwing error, and run stopped after a time.
>
> vlimit exceeded for step 3680; vmax = 290.4790
> vlimit exceeded for step 3681; vmax = 5167.6693
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 2017 4081 4082
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> So, please give some tips so as I can complete it.
>
> Thanking you
> Sanjib
>
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Received on Wed Jun 20 2012 - 05:30:03 PDT
