Dear sir,
Many thanks for your response.
I visualized the output file "com_solvated.pdb" using chimera software.
The bond between carbon and chlorine atoms are missing in visualization.
However, the bonds to othet atom are intact and it is intact in input file
of ligand also.
Thanks & Regards
Ramesh
On Feb 20, 2015 1:13 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> 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 - 03:30:04 PST
