[AMBER] Virtual Spin Labels in Amber

From: Kari Gaalswyk <kari.gaalswyk.ucalgary.ca>
Date: Thu, 10 Jan 2019 15:56:30 +0000

Dear Amber Users,

I am trying to incorporate a virtual spin label into a protein following the approach done by Islam et. al. (S. M. Islam, R. A. Stein, H. S. Mchaourab, B. Roux, J. Phys. Chem. B 2013, 117, 4740–4754.) using leap. I will then solvate the system and use the .prm and .mdcrd files as input for MD in OpenMM. In order to allow for multiple spin labels in a protein, and to better keep track of them, I’ve created new definitions for each residue that contain the virtual spin label (OND) bound to the Calpha. I have modified the leaprc and frcmod files for the f14SB force field, and created a lib file for the new residue definitions (for testing purposes, the lib file is only a modified alanine named ONA). The modifications to the leaprc file are:


addAtomTypes {


{“OND”, “ON”, “sp3”} //new atom type

frcmod14SB = loadamberparams frcmod.ff14SB_OND //changed the frcmod file

loadOff ala_OND.redq.lib //new lib file


The changes to the frcmod file resemble those in the Islam et. al. paper (see SI). We treat it very similar to an oxygen:



ON 16.00 0.000


CX-ON 1.2 8.0


C -CX-ON 2.0 46.0

CT-CX-ON 2.0 46.0


N-CX-C-ON 1.9 1 240.0

N-CX-CT-ON 1.9 1 240.0


ON 2.0000 0.0500


The new lib file is a modification of the amino12.redq.lib file (for testing it only contains a modified alanine residue). The relevant lines are:




“OND” “ON” 0 1 131072 11 0 0.0



“OND” “ON” 0 -1 0.0



3 11 1 //CA and OND



2.552251 8.382596 6.463704


The positions were determined using the following equations:

direction = (ca_pos – cb_pos) / np.linalg.norm(ca_pos – cb_pos)

ond_pos = (direction + ca_pos – n_pos)

When I try to create an alanine chain with a modified residue from sequence, I get a fatal error related to chirality:


Welcome to LEaP!

(no leaprc in search path)

> source leaprc.ff14SB_OND.redq

----- Source: ./leaprc.ff14SB_OND.redq

----- Source of ./leaprc.ff14SB_OND.redq done

Log file: ./leap.log

atom type OND - unknown element ON

Loading parameters: /home/kari.gaalswyk/anaconda2/bin/../dat/leap/parm/parm10.dat

Reading title:

PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA

Loading parameters: ./frcmod.ff14SB_OND2

Reading force field modification type file (frcmod)

Reading title:

ff14SB protein backbone and sidechain parameters

Loading library: /home/kari.gaalswyk/anaconda2/bin/../dat/leap/lib/amino12.redq.lib

Loading library: /home/kari.gaalswyk/anaconda2/bin/../dat/leap/lib/aminoct12.redq.lib

Loading library: /home/kari.gaalswyk/anaconda2/bin/../dat/leap/lib/aminont12.redq.lib

Loading library: /home/kari.gaalswyk/anaconda2/bin/../dat/leap/lib/nucleic12.redq.lib

Loading library: ./ala_OND.redq.lib

.database.c 515|WARNING: Nonunique entry in database: !index found

.database.c 515|WARNING: Nonunique entry in database: entry.ON.unit.connect found

Loading library: /home/kari.gaalswyk/anaconda2/bin/../dat/leap/lib/atomic_ions.lib

Loading library: /home/kari.gaalswyk/anaconda2/bin/../dat/leap/lib/solvents.lib

> foo = sequence {ALA ALA ALA ONA ALA ALA}

ERROR: Comparing atoms

.R<ONA 4>.A<C 9>,

.R<ONA 4>.A<CB 5>,

.R<ONA 4>.A<HA 4>, and

.R<ONA 4>.A<N 1>

to atoms

.R<ONA 4>.A<C 9>,

.R<ONA 4>.A<CB 5>,

.R<ONA 4>.A<OND 11>, and

.R<ONA 4>.A<N 1>

This error may be due to faulty Connection atoms.

!FATAL ERROR----------------------------------------

!FATAL: In file [chirality.c], line 142

!FATAL: Message: Atom named OND from ONA did not match !




I get the same error if I try to load a pdb file with the modified residue already incorporated (both with and without the OND atom present). From my understanding, this is because I have defined a pentavalent carbon (by bonding it to the Calpha in the lib file), and the chirality functions are attempting to match the 4 neighbors of the CA, but it now has 5. Is there any way to allow for pentavalency in tleap, or am I going about this the wrong way? I’m not too familiar with amber’s inner workings.

Thank you,

Kari Gaalswyk
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Received on Thu Jan 10 2019 - 08:00:05 PST
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