[AMBER] Missing CMAP entries in prmtop in multiple calls to sequence

From: Evan Pretti via AMBER <amber.ambermd.org>
Date: Tue, 1 Apr 2025 00:11:44 +0000

Hello,

I am encountering an issue when trying to construct some systems using LEaP and ff19SB. Using multiple calls to the sequence command to construct the system sometimes causes CMAP entries to be omitted from the resulting prmtop. I originally encountered this in the context of using GLYCAM’s modified residues for glycosylation, but the following minimal reproducing example does not require this to observe the problem.

The following tleap input:

source leaprc.protein.ff19SB
test = sequence { ACE ALA ALA NME }
saveAmberParm test test.top test.crd
quit

produces a prmtop with the expected 2 CMAP entries given the two ALA residues present:

...
%FLAG CMAP_INDEX
%FORMAT(6I8)
       5 7 9 15 17 1
      15 17 19 25 27 1

However, the following tleap input:

source leaprc.protein.ff19SB
test = sequence { ACE ALA }
test = sequence { test ALA }
test = sequence { test NME }
saveAmberParm test test.top test.crd
quit

causes the prmtop to be missing 1 of the 2 CMAP entries:

...
%FLAG CMAP_INDEX
%FORMAT(6I8)
      15 17 19 25 27 1

I am using AmberTools 24.8 from conda-forge. Apologies if this is a known issue that I failed to find in a search through the archive.

Thanks,
Evan Pretti
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Received on Mon Mar 31 2025 - 17:30:02 PDT