Dear Saikat,
At this pH your titratable residues are likely all protonated. You may run a short CpHMD simulation to make sure. Thus, you should be safe running a regular MD simulation as long as you properly choose the protonated form of the titratable residues when you prepare your prmtop and inpcrd files in tleap.
I hope this helps,
Best regards,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Saikat Pal <saikatpaliitg.yahoo.com>
Sent: Friday, February 8, 2019 10:29:38 AM
To: AMBER Mailing List
Subject: [AMBER] Regarding constant pH MD
Dear all,
I have a peptide PDB at pH 1.8. I want to study the structural change of the peptide at pH 1.8. Should I run const pH simulation or normal MD simulation?Any suggestion is highly appreciated.
Thanks and Regards,
Saikat Pal
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Received on Mon Feb 11 2019 - 07:30:06 PST
