[gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

[Justin Lemkul]

On 8/13/17 12:47 PM, ZHANG Cheng wrote:
> Hi Justin,
> Thank you for explaining that.
> 
> 
> You said "a more reliable system", what does this mean? It is my first time adding glycines to my protein using OPLS-AA/L force field. Do you think this might be the reason, and should I switch to another force field?
> 

I'm talking about hardware.  Failure to write a valid frame is usually due to a 
filesystem problem (i.e. hard disk).  It doesn't matter what your force field is 
or what your system contents are.

> 
> My procedure is as follows:
> 1) I get the glycine and protein pdb, convert them to .gro files using
> gmx pdb2gmx -f glycine/protein.pdb -o glycine/protein.gro -water spce -inter
> 2) then I add the protein.gro into a box, get the protein_newbox.gro:
> gmx editconf -f protein.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
> 3) then I add glycines to this box:
> gmx insert-molecules -ci glycine.gro -nmol 203 -f protein_newbox.gro -o protein_203_glycine.gro
> 4) then I do the exactly the same thing according to your tutorial, i.e. solvent with water, add ions, energy minimization, NVT, NPT, and finally the MD.
> 
> 
> Can I ask if the procedure is correct? Would you please recommend some tutorial for prepare a system with protein and excipients (e.g. glycine, sorbitol, etc)?
> 

It's fine.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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