Re: [AMBER] Regarding constant pH MD

From: Cruzeiro,Vinicius Wilian D <>
Date: Mon, 11 Feb 2019 15:08:59 +0000

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 <>
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
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