[gmx-users] problem in energy minimization

[Abhik Mukhopadhyay]

Hi Jastin
My pdb2gmx command line is 
pdb2gmx -ignh -f xx.pdb -o xxout.pdb -p xx.top -water spce

When I created the topology it did not create a bond between those two residues (between which the part is missing).

Thanks for your suggestion.
Abhik

Abhik Mukhopadhyay
  Departamento Química / Faculdade de Ciências e Tecnologia 
 Universidade Nova de Lisboa , 2829-516 Caparica, Portugal 

Mob. 00351912991251
  http://xtal.dq.fct.unl.pt/



--- On Thu, 3/12/09, Justin A. Lemkul <jalemkul at vt.edu> wrote:
From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] problem in energy minimization
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, March 12, 2009, 7:54 PM


Abhik Mukhopadhyay wrote:
> Hi everyone,
> I am trying to run a simulation on a xray structure that has 15 residues
missing. I have made the topology file accordingly. But after energy
minimization, the residues between which the portion is missing, got connected.
I tried an energy minimization with all-bonds constraint, but that i guess did
not do it properly.
> This is the last part of the minimization run
> 

When you created the topology, did pdb2gmx add a bond between the residues
flanking the missing residues?  What was your pdb2gmx command line?

If you are sure that the missing residues will not influence the dynamics
(think carefully!), then read in the manual about distance restraints.  If you
have difficulties implementing these restraints, there are dozens of posts in
the list archive that should guide you in how to use them.

-Justin

> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> 
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> writing lowest energy coordinates.
> 
> Back Off! I just backed up ccpox_em.trr to ./#ccpox_em.trr.1#
> 
> Back Off! I just backed up ccpox_b4pr.pdb to ./#ccpox_b4pr.pdb.1#
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -2.2785961e+05
> Maximum force     =  5.1547680e+08 on atom 1004
> Norm of force     =  8.2600877e+08
> 
> My question is how can I run a simulation on these structure keeping that
part as it is?
> 
> Thanking you in advance.
> Abhik
> 
> 
> 
>  
> *Abhik Mukhopadhyay
> *
> Departamento Química / Faculdade de Ciências e Tecnologia
> Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
> 
> Mob. 00351912991251
> http://xtal.dq.fct.unl.pt/
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- ========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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