[gmx-users] lipopeptide problem

[Emine Deniz Tekin]

Hi Felix,
Thank you for your help.

Hi Justin,

I did not want to write a long e-mail describing what I did and what did not
work. All I wanted to learn was whether there was some more detailed
information somewhere that I can reach. You do not have to reply to an email
if you feel it is not worth it. Lecturing me on "willingness" is crossing
the line. How do you know how much I tried? Anyhow, thanks for your earlier
help, but you can simply skip my future postings.

Best regards,

Deniz


On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Emine Deniz Tekin wrote:
>
>> Hi GROMACS Users,
>>
>> I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I
>> simulated a peptide before but this is the first time I am trying to combine
>> a lipid with a peptide (to get a lipo-peptide). I would be really happy if
>> you could help me out with the following question
>>
>> I am tring to create a louroic acid connected to and an 8-redidue peptide.
>> To create residues, I used ARGUSLAB . For the louric acid I used BERGER
>> lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined
>> ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the
>> topol.top files as described in the manual. But this procedure did not yet
>> give me an attached louric acid and peptide. I
>>
>
> Nor should you expect it to.  Building the parent force field does not give
> you a topology describing some molecular system.
>
>
> still have to play with the aminoacids.hdb, aminoacids.rtp,
>> residuetypes.dat, atomtypes.atp, and specbond.dat files. I would appreciate
>> if you could let me know how to modify these files, especially the
>> aminoacids.hdb file. I tried several things but it not
>>
>
> See the manual, section 5.6.4.  The contents and format are discussed at
> length.
>
>
> work. Note that, I applied the suggestions in
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
>> but it was not sufficient.
>>
>>
> If you want free help, you will have to do substantially better than "it
> was not sufficient."  What is not clear?  What have you tried and what was
> the result? If you want free help, you've got to demonstrate a willingness
> to do some work on your own.
>
> -Justin
>
> Best regards
>>
>> Deniz
>>
>>
> --
> ========================================
>
> 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
>
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