[gmx-users] .pdb to .gro => the atoms are not conneced with VMD

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Sun Oct 5 14:11:22 CEST 2008


VMD uses a heuristic method to know if some atoms are connected. Sometimes the method fails. To be sure (and see) the atoms are well connected in VMD, you need to provided a psf file with your pdb/gro in VMD. So in your case you gro files is correct (since you indicated that your system are correct). An alternative see you gro in other software in pymol to confirm. 

I hope it helps 



Stéphane Abel, PhD
91191 Saclay, FRANCE
website: http://www.st-abel.com


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Today's Topics:

   1. PR after minimisation and PR of missing residues? (minnale )
   2. .pdb to .gro => the atoms are not conneced with VMD
      (Chih-Ying Lin)


Message: 1
Date: 5 Oct 2008 05:26:52 -0000
From: "minnale " <minnale_gnos at rediffmail.com>
Subject: [gmx-users] PR after minimisation and PR of missing residues?
To: "gmx-users1" <gmx-users at gromacs.org>
Message-ID: <20081005052652.29962.qmail at f5mail-236-241.rediffmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi all,
  I have two doubts on PR, may be these are trivial to you.

1.According to Gromacs procedure(from Gromacs tutorial) the sequential steps are (a)Energy minimisation (b)Position restrain with force constant descendant manner and finally (c)production. Here my doubt that, is it require to do energy minimisation between PR and production? because after PR the system equilibrating properly if do one minimisation the structure looses bad contacts with low energy, am I right?  

2.If my desire protein contain some missing residues(from PDB)rectified those residues by using INSIGHT-II. Later start simulations particularly at PR, is it require to keep restrain specifically on added missing residues or whole protein residues in .itp file?      

Any suggestions would be appreciated

Thanks in advance.
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Message: 2
Date: Sun, 5 Oct 2008 01:53:36 -0700
From: "Chih-Ying Lin" <chihying2008 at gmail.com>
Subject: [gmx-users] .pdb to .gro => the atoms are not conneced with
To: gmx-users at gromacs.org
	<5777f3840810050153q6922b1d8u8ef6ccdd8fba7859 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

I make .pdb file to .gro file.

With the VMD, the atoms are seen NOT conneced.

Is there any possible errors in my .gro file?



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