[AMBER] Help to generate prmtop and .crd files from a PDB trajectory

From: Devlina Chakravarty <devlina.chakravarty.gmail.com>
Date: Mon, 25 Jan 2021 20:46:03 -0500


I need to perform MMPBSA analysis on a protein complex, I only have the
trajectory in a PDB format (as in models 1 to N depicting frames of the
simulation). To run MMPBSA I need to generate topology files for the
complex, the receptor, and ligand separately, as well as the trajectory
file following the tutorial on Ras-Raf complex from Amber (

For the first step I generated the AMBER .crd trajectory using the first
model/frame from the PDB trajectory as a parameter file and the following
CPPTRAJ commands:

parm top_model.pdb

trajin 6vw1-0-trj_25ns_transMD1.pdb 1 last 40


rms first mass .CA

trajout 6vw1_nat_md1.crd nobox




Then, I have leap to generate topology files for the complex, receptor, and
the ligand


source leaprc.protein.ff14SB

loadamberparams gaff.dat

a = loadPdb top_model.pdb

check a

set default PBRadii mbondi2

saveAmberParm a 6vw1_nat1.top 6vw1_nat1.crd

savepdb a 6vw1-leap.pdb

b = loadPdb top_model1_A.pdb

saveAmberParm b 6vw1_nat1_A.top 6vw1_nat1_A.crd

c = loadPdb top_model1_B.pdb

saveAmberParm c 6vw1_nat1_B.top 6vw1_nat1_B.crd



The problem is when I tried to visualize the .top and .crd file on VMD,
there are strange artifacts and connections that shouldn't be there, like
the first residue of the second chain is connected to the last residue to
the first chain (although the PDB file used to generate the topology file
has TER in between the two chains). I have removed all HETATMs and hydrogen
atoms from the PDB files before using them in leap and cpptraj. I have also
renumbered the residues to make them continuous starting from 1. I am not
sure how to fix this issue, where am I going wrong. Any help will be
greatly appreciated,

Thank you,

Devlina Chakravarty
Postdoctoral Associate
Department of Chemistry
Rutgers University - Camden
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Received on Mon Jan 25 2021 - 18:00:02 PST
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