You do not show any error message but merely some harmless warning of a close contact. How have you concluded that bonds are broken or coordinates are missing?
________________________________________
From: Shreeramesh [shreeramesh.gmail.com]
Sent: 20 February 2015 10:58
To: AMBER Mailing List
Subject: [AMBER] Error while running tleap for the ligand containing two chlorine atoms
Dear All,
I am running tleap for a ligand containing two chlorine atoms using the
following tleap script
Script:
source leaprc.ff14SB
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
LIG2 = loadmol2 LIG2.mol2
loadamberparams LIG2.frcmod
check LIG2
loadamberparams frcmod.ionsjc_tip3p
complex = combine {LIG LIG2}
set default PBRadii mbondi2
saveAmberParm LIG LIG.top LIG.crd
saveAmberParm LIG2 LIG2.top LIG2.crd
saveAmberParm complex com.top com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Na+ 0
solvatebox complex TIP3PBOX 8.0
saveAmberParm complex com_solvated.top com_solvated.crd
savepdb complex com_solvated.pdb
quit
In the output of "*com_solvated.pdb*", the bond between carbon and chlorine
atoms are broken with the following errors
Further, the coordinates are incomplete in the following file: "complex
com_solvated.top" and "com_solvated.crd"
*Error:*
Reading title:
remark goes here
Checking 'LIG'....
Warning: Close contact of 1.413440 angstroms between .R<CLM 1>.A<HC1 25>
and .R<CLM 1>.A<HC5 29>
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
I request you to kindly help me in solving the above mentioned error
Thanks & regards
*Ramesh M*
Email: shreeramesh.gmail.com
Mobile: 91 + (0) 9646469938 27+ (0) 844556164
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Received on Fri Feb 20 2015 - 03:30:03 PST
