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Today's Topics:
1. Re: How to remove H atom from residue in gro file?
(Justin A. Lemkul)
2. Re: How to remove H atom from residue in gro file? (Mark Abraham)
3. Re: Number of coordinate in topol.top and solv.gro not
matching (Justin A. Lemkul)
4. Re: Automation of selecting water around a molecule (Mark Abraham)
5. ? (Shima Arasteh)
6. Re: GROMOS87 and CHARMM27 (Justin A. Lemkul)
--
Message: 1
Date: Wed, 02 May 2012 09:09:39 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] How to remove H atom from residue in gro
file?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4fa13213.2040...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/2/12 6:55 AM, Hagit G wrote:
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with
a
disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore it because *each cystein
is
on a different chain*. So it adds H and therefor the disulfide bond is ruined
during energy minimization.
Is there any way to recreate such a disulfide bond (Please don't tell me
again
about -ss it works only on one chain. Moreover, the bond is existed on the
pdf
file.) or never ruined it at the first place?
Well you may need to use -ss, but since you don't want to hear about it, I
won't
say anything more...
What you need to do is create a [moleculetype] that consists of both chains.
The pdb2gmx option -chainsep will allow you to create a properly merged
molecule
that can form the intermolecular disulfide because the two molecules will be
considered as one [moleculetype], as Gromacs requires.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
Message: 2
Date: Wed, 02 May 2012 23:11:08 +1000
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] How to remove H atom from residue in gro
file?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4fa1326c.6080...@anu.edu.au
Content-Type: text/plain; charset=iso-8859-1
On 2/05/2012 8:55 PM, Hagit G wrote:
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains
connected with a disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore it because *each
cystein is on a different chain*. So it adds H and therefor the
disulfide bond is ruined during energy minimization.
Is there any way to recreate such a disulfide bond (Please don't tell
me again about -ss it works only on one chain. Moreover, the bond is
existed on the pdf file.) or never ruined it at the first place?
Yes, and the clue to how to combine the chains to give the mechanism a
chance of working is on the page I linked last time:
http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds
Mark
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Message: 3
Date: Wed, 02 May 2012 09:12:13 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Number of coordinate in topol.top and
solv.gro notmatching
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4fa132ad.1060...@vt.edu
Content-Type: text/plain; charset=UTF-8; format=flowed
On 5/2/12 8:14 AM, Sangita Kachhap wrote:
Hello all
I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
I have used following command:
pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
grompp -f em.mdp
