[gmx-users] RE: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

On 6/12/12 12:09 PM, Erica Hicks wrote:
> Hi,
>
> I am still working on this error but found that a possible error could be the way editconf was used to convert .pdb to .gro in Step 3. I used the command:
>
> editconf -f dppc128.pdb -o dppc128.gro
>
> Is this correct? Would it have been better to use pdb2gmx, instead? ( pdb2gmx –f input.pdb –o output.gro -o protein.top –inter ) Why use editconf?
>

Because all that's needed here is a file format conversion.  Parameters for DPPC 
are not present in most force field .rtp files, so pdb2gmx will throw a fatal 
error.  The job of pdb2gmx is to write a topology; outputting a coordinate file 
is more or less a side effect.  Since we already have a topology for DPPC, and 
the coordinate file matches but simply needs to be in a different format, 
editconf is the easiest solution.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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