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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"
> Subject: Re: [gmx-users] How to remove H atom from residue in gro
> file?
> To: Discussion list for GROMACS users
> 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
> Subject: Re: [gmx-users] How to remove H atom from residue in gro
> file?
> To: Discussion list for GROMACS users
> 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
> -- next part --
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> --
>
> Message: 3
> Date: Wed, 02 May 2012 09:12:13 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Number of coordinate in topol.top and
> solv.gro notmatching
> To: Discussion list for GROMACS users
> 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 -