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

From: Daniel Roe <>
Date: Thu, 28 Jan 2021 10:03:28 -0500


On Mon, Jan 25, 2021 at 8:46 PM Devlina Chakravarty
<> wrote:
> 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

PDB files contain only very limited topology (i.e. connectivity)
information - most of it is inferred. Programs like VMD and cpptraj
try to do their best to determine the missing information, but if the
structure has problems (is distorted, missing residues, etc) this can
fail. Your best bet may be to actually build the system and generate a
topology (via e.g. pdb4amber and leap) and use that in place of the
original pdb.

Good luck,


> 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
> --
> Devlina Chakravarty
> Postdoctoral Associate
> Department of Chemistry
> Rutgers University - Camden
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> AMBER mailing list

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Received on Thu Jan 28 2021 - 07:30:02 PST
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