[gmx-users] genbox

shahid nayeem msnayeem at gmail.com
Wed Apr 21 14:27:26 CEST 2010 

I was also trying to put more than one protein in one simulation box. I was
able to do it with genconf but it appears that the addition is in very
ordered manner if one looks .gro file in VMD. How can I add these protein in
disordered random orientation.
msnayeem


On 4/20/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> fahimeh bafti wrote:
>
>> Thanks :)
>> but I couldn't manage with that, it makes the same error with editconf as
>> well, the problem was related to having more than one residue inside
>> insert.gro
>>
>
> editconf should not have a problem placing multi-residue molecules within a
> box.  That is its main function, so I can only assume you did something
> wrong.
>
> I did it at the end with genconf
>>
>> genconf  -nbox 2 2 2 (as u want)  -f  file.gro  -o file_replicate.pdb
>>
>> it will simply replicate the unit.
>>
>>
> That works.  Glad you found a solution.
>
> -Justin
>
>  Fahimeh
>>
>>  > Date: Tue, 20 Apr 2010 09:12:44 -0400
>>  > From: jalemkul at vt.edu
>>  > To: gmx-users at gromacs.org
>>  > Subject: Re: [gmx-users] genbox
>>  >
>>  >
>>  >
>>  > fahimeh bafti wrote:
>>  > > Thank you Justin
>>  > > but I end up with a new error. now in the insert.pdp file I have a
>>  > > molecule which I need to add 4 copy of that inside the solute.pdb
>>  > > genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb
>>  > >
>>  > > but it gave me:
>>  > >
>>  > > Fatal error:
>>  > > more then one residue in insert molecules
>>  > > program terminated
>>  > >
>>  >
>>  > Then you have two options:
>>  >
>>  > 1. Use the development (git) version of the code, which I believe can
>> now deal
>>  > with multi-residue molecules.
>>  > 2. Use editconf to position all the components of your system.
>>  >
>>  > You could, I suppose, hack your "insert.pdb" to contain one residue
>> (i.e.,
>>  > through renaming and renumbering) and then convert it back, but that
>> sounds like
>>  > a mess. Probably #2 is the easiest.
>>  >
>>  > -Justin
>>  >
>>  > > Fahimeh
>>  > >
>>  > >
>>  > > > Date: Tue, 20 Apr 2010 07:10:59 -0400
>>  > > > From: jalemkul at vt.edu
>>  > > > To: gmx-users at gromacs.org
>>  > > > Subject: Re: [gmx-users] genbox
>>  > > >
>>  > > >
>>  > > >
>>  > > > fahimeh bafti
>>  > > > > Hello,
>>  > > > >
>>  > > > > I want to use a file.pdb which has 8 chain of polypeptide, each
>> chain
>>  > > > > contains 6 residues. I need to expand it to 12 chains of 6
>> rsidues
>>  > > so I
>>  > > > > need to add 4 chains or in the other word 24 residues. I think I
>>  > > have to
>>  > > > > use genbox, so I make another copy of file.pdb and rename it to
>>  > > > > insert.pdb and i used this command, but it doesn't work.
>>  > > > >
>>  > > > > genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro
>>  > > > >
>>  > > > > can anybody help me?
>>  > > >
>>  > > > The implication with genbox -ci -nmol is that the coordinate file
>>  > > passed to -ci
>>  > > > contains one molecule, and an additional -nmol molecules are
>>  > > inserted. So if
>>  > > > you already have 8, you need a coordinate file with one polypeptide
>>  > > and then:
>>  > > >
>>  > > > genbox -ci insert.pdb -nmol 4
>>  > > >
>>  > > > Note in the documentation that -nmol refers to the number of
>>  > > molecules, not a
>>  > > > number of residues, which I think is the root of your problem.
>>  > > >
>>  > > > -Justin
>>  > > >
>>  > > > >
>>  > > > > Fahimeh
>>  > > > >
>>  > > > >
>>  > >
>> ------------------------------------------------------------------------
>>  > > > > Hotmail: Trusted email with powerful SPAM protection. Sign up
>> now.
>>  > > > > <https://signup.live.com/signup.aspx?id=60969>
>>  > > > >
>>  > > >
>>  > > > --
>>  > > > ========================================
>>  > > >
>>  > > > 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
>>  > > >
>>  > > > ========================================
>>  > > > --
>>  > > > gmx-users mailing list gmx-users at gromacs.org
>>  > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>  > > > Please search the archive at http://www.gromacs.org/search before
>>  > > posting!
>>  > > > Please don't post (un)subscribe requests to the list. Use the
>>  > > > www interface or send it to gmx-users-request at gromacs.org.
>>  > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>  > >
>>  > >
>> ------------------------------------------------------------------------
>>  > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection.
>> Sign
>>  > > up now. <https://signup.live.com/signup.aspx?id=60969>
>>  > >
>>  >
>>  > --
>>  > ========================================
>>  >
>>  > 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
>>  >
>>  > ========================================
>>  > --
>>  > gmx-users mailing list gmx-users at gromacs.org
>>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>  > Please search the archive at http://www.gromacs.org/search before
>> posting!
>>  > Please don't post (un)subscribe requests to the list. Use the
>>  > www interface or send it to gmx-users-request at gromacs.org.
>>  > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> ------------------------------------------------------------------------
>> Hotmail: Powerful Free email with security by Microsoft. Get it now. <
>> https://signup.live.com/signup.aspx?id=60969>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100421/09471daa/attachment.html>

More information about the gromacs.org_gmx-users mailing list