Faezeh Kargar wrote:
Dear Justin
Thank you for your reply. this simulation contains a peptide and water
in a specified pH. Do you think this .pdb file is correct.
I have no way to assess whether or not it is correct. As I have already told
you, it is a plausible input file. Beyond that, I cannot say, nor can anyone
else but you.
-Justin
Thank you
Kargar
>
>
> Faezeh Kargar wrote:
>> Dear All
>>
>> I asked this question in Martini's forum, but tile now no answer, so I
>> had to ask it here. excuse me.
>> I did an atomistic peptide simulation. The residues and positions of
>> all atoms in this peptide created by my self, I mean I didn't download
>> the pdb file from <www.pdb.org>. at the end of atomistic simulation I
>> have .pdb and .gro files that show the minimized structure of the
>> peptide.
>>
>> Now I have a question: Can I use the last pdb file for a CG peptide?
Can
>> I use atom2cg.awk and seq2itp.pl in this case?
>>
>
> You can run those scripts on any syntactically-correct .pdb file.
>
> -Justin
>
>> Thank you
>> Kargar
>>
>
> --
> ========================================
>
> 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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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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