[gmx-users] MD Simulation of DPPC Lipid Bilayer

[Nancy]

I tried to follow the "Membrane Protein" tutorial at:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

I downloaded the "properly oriented" PDB file of the KALP-15 model peptide:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/KALP-15_princ.pdb

I then attempted to run the pdb2gmx command:

pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc

For the force field, I chose #4, the "GROMOS96 53a6 force field", as well as
"None" for the termini, as stated in the tutorial.  However, pdb2gmx outputs
the following error message:

-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 17 while adding improper
-------------------------------------------------------

Please let me know how I should go about this.

Thanks,

Nancy



On Tue, Jul 28, 2009 at 1:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Quoting Nancy <nancy5villa at gmail.com>:
>
> > Hello,
> >
> > I am new to Gromacs, but have prior experience with MD simulations.  I'd
> > like to setup and run a simulation of hydrated
> > dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature
> > (~298 K).  Are there tutorials that provide step-by-step instructions on
> how
> > to do this?
> >
>
> Not directly, but there are several resources available.  Step 1 should
> certainly be Chapter 5 of the manual, to understand how to construct the
> topology of your system, since pdb2gmx will not do it for you.  Other than
> that, there are general references online:
>
> http://oldwiki.gromacs.org/index.php/Membrane_Simulations
>
> There is also a plethora of question/answer threads in the list archive,
> which
> can be searched through the online interface:
>
> http://oldwww.gromacs.org/swish-e/search/search2.php
>
> Structures and topologies can be downloaded from a number of research group
> webpages, many of which are cited in the literature and mentioned in the
> archived discussions.
>
> -Justin
>
> > Thank you.
> >
> > Nancy
> >
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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