AMBER: xleap with modified residue

From: Whitney Allen <>
Date: Thu, 20 Oct 2005 11:12:42 -0700 (PDT)

Hi Amber users

I am trying to run MD on a TRNA structure (6tna.pdb). This molecule has several modified bases and so I have used Antechamber to compute a molecule library for each modified base. However, after loading the library file into xleap (which is successful) I try and load the TRNA structure and xleap completely shuts down.

Below is the procedure that I follow. Note that I have tried to follow tutorials 4 & 5 as applicable. Here, for simplicity, I have cut the TRNA PDB file so that it contains only one modified residue (2MG or residue 10 in the 6tna.pdb file) and 15 total residues (residues 1-15 in the 6tna.pdb file) and have called it test.pdb. If anyone can help please reply and I can send you the 2MG.pdb, 2MG.mol2, 2mg.lib, and test.pdb files.


(Antechamber- note that I change the residue to a molecule)


% $AMBERHOME/exe/antechamber -i 2MG.pdb -fi pdb -o 2MG.mol2 -fo mol2 -c bcc -s 2 -mk "CARTESIAN AM1 STANDARD DIRECT OPT=LBFGS XTEST=0.0001"


% $AMBERHOME/exe/parmchk –i 2MG.mol2 –f mol2 –o 2MG.frcmod


% xleap –f leaprc.rna.ff99

source leaprc.gaff

loadmol2 2MG.mol2

check 2MG

edit 2MG

loadamberparms 2MG.frcmod

check 2MG

saveoff 2MG.lib

desc 2MG



% xleap –f leaprc.rna.ff99

source leaprc.gaff

loadoff 2mg.lib

check 2MG

mol=loadpdb test.pdb


(At this point xleap closes and I get the following error)


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

!FATAL: In file [chirality.c], line 120

!FATAL: Message: Atom P is not in the first list




Please help me understand what is going on here and let me know how I can get this to work. It looks like all of the files are of normal format so I am a bit confused.

Thanks in advance

Whitney Hastings

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Received on Thu Oct 20 2005 - 19:53:01 PDT
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