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 jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] problem in energy minimization
To: Discussion list for GROMACS users gmx-users@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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