AMBER Archive (2008)

Subject: RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 29 2008 - 15:57:21 CDT

Dear Saurabh,

 

The *’s mean that the value is too large to fit in the space provided. In this case your electrostatics are huge. If you look at step 400 you see that the maximum gradient is a huge 10^12 Kcal/mol/A2. This force is on atom Se1 number 761 which is your Selenium atom. What showed earlier implied that things looked good on step 1. I.e. none of the energies looked to be too big so your initial structure is probably okay. It is the minimization itself that is causing the problem. I suspect that your parameters for selenium are not good. In particular the VDW parameters may be wrong such that this atom can approach very very close to another atom and then giving huge EEL energies. It is also possible that you have some strange bond term in there with an inappropriate equilibrium bond length or the charge is set wrong on the selenium.

 

I think you will need to do some careful investigation here to work out what is wrong. I would start by just minimizing the ligand itself in gas phase without the protein or water there. This will help you track down what is wrong with the selenium. You should then inspect all the parameters carefully and make sure you can get things working for just the ligand before proceeding.

 

During the minimization I would start by doing just 400 steps of steepest descent. Set ntwr=-1 and then you will get a restart file for every minimization step. You can then load this into something like VMD and watch what actually happens.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of saurabh agrawal
Sent: Saturday, April 26, 2008 7:16 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...

 

Dear Sir,

Thanks for the suggestions. On increasing the SD runs to 1800 followed by 200 CG runs system runs fine at restraint value 20.

For the same minimization run when I reduced the restraint to 10 it gives following output and aborts.

NSTEP ENERGY RMS GMAX NAME NUMBER
    400 -1.0822E+07 1.0884E+10 1.0151E+12 Se1 761
 
 BOND = 2465.6712 ANGLE = 212.0772 DIHED = 581.1697
 VDWAALS = 3738.4993 EEL = ************* HBOND = 0.0000
 1-4 VDW = 208.1155 1-4 EEL = -1701.6655 RESTRAINT = 25.4368
 EAMBER = *************
 
 
   NSTEP ENERGY RMS GMAX NAME NUMBER
    500 -3.5333E+07 1.1667E+11 1.0880E+13 N1 783
 
 BOND = 2465.6719 ANGLE = 212.0774 DIHED = 581.1696
 VDWAALS = 3738.4993 EEL = ************* HBOND = 0.0000
 1-4 VDW = 208.1156 1-4 EEL = -1701.6655 RESTRAINT = 25.4369
 EAMBER = *************

Please give your kind suggestion.

Thanking you in advance.

saurabh

--- On Sat, 26/4/08, Barbault Florent <florent.barbault_at_paris7.jussieu.fr> wrote:

From: Barbault Florent <florent.barbault_at_paris7.jussieu.fr>
Subject: Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...
To: amber_at_scripps.edu
Date: Saturday, 26 April, 2008, 6:43 PM

Hello,

  

This problem happens commonly also with me. If you use a combinaison

of steepest descent followed by conjugate gradient, I suggest that you

increase the number of SD steps. Generally it works fine.

Regards

Florent Barbault

  

On Sat, 26 Apr 2008 17:06:13 +0530 (IST)

  saurabh agrawal <imsam100_at_yahoo.co.in> wrote:

> Dear Amber Users,

>

> I am trying to simulate nucleotide ligand complex. But It aborted

>during the simulation once I reduce the restraints below 20 in the

>input file and gives the following error.

>

> NSTEP ENERGY RMS GMAX NAME

> NUMBER

> 900 NaN NaN
 0.0000E+00 H5T

> 1

>

>

>

> BOND = NaN ANGLE = NaN DIHED = NaN

> VDWAALS = -140.5901 EEL = NaN HBOND =

> 0.0000

> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN

> EAMBER = NaN

>

>

>

>

>

>

> NSTEP ENERGY RMS GMAX NAME

> NUMBER

> 1000 NaN NaN
 0.0000E+00 H5T

> 1

>

>

>

> BOND = NaN ANGLE = NaN DIHED = NaN

> VDWAALS = -140.5901 EEL = NaN HBOND =

> 0.0000

> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN

> EAMBER = NaN

>

>

>

> .... RESTARTED DUE TO LINMIN FAILURE ...

>

>

>

> .... RESTARTED DUE TO LINMIN FAILURE ...

>
                                        

>

>

> .... RESTARTED DUE TO LINMIN FAILURE ...

>

> The same nucleotide I have simulated with different ligands and

>those run fine. This ligand is having two Selenium atoms (which is

>not defined in the leap). Is this the reason for the problem?

>

> Every time it is stopping, and I am unable to solve it.

>

> Please help me in this regard.

>

> saurabh

>

> From Chandigarh to Chennai - find friends all over India.

> Click here.

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