iitdckc at gmail.com
Fri Aug 13 17:11:28 CEST 2010
Chandan kumar Choudhury
On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> abdullah ahmed wrote:
>> I'd like to ask a question about the conversion of the results of
>> minimization to pdb format. Here is what I do:
>> 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top
>> (pdb2gmx -f -p -o)
>> 2. Run editconf to define the box (editconf -d 1)
>> 3. run gromp and mdrun for the minimization
> use mdrun -c . It will give you the required pdb file
> 4. Run editconf to re-convert back to pdb
>> Unfortunately doing this seems to be adding some information into the pdb
>> file that is not related to the atom coordinates. I think this might be
>> trajectory data. Is there someway to remove this info?
> What is it exactly that you're seeing? The output .gro file from mdrun
> (which can be output as .pdb directly, if you prefer) contains only
> coordinates and box vectors, so anything else should just be comment lines.
> Thank you in advance,
> 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
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