First of all, if you expect someone to reproduce your problem make sure that the input you provide can actually be run. Your leap script has filenames in uppercase while what you have attached is in lower case, frcmod files are missing etc. Please test this before you send files and please also pack this up into a single archive file.
I see Cl1 and Cl2 as atoms 8 and 9. But this is nor really relevant, you are not using this for simulation, are you? What do your _topology_ files contain i.e. the files you name as *.top? Check if they have the right GAFF atom types.
And again, your PDB file does not contain connectivity information. Whatever your visualisation program shows has been computed and may not be the same as in your _topology_ file. So try e.g. vmd loading the _topology_ file in connection with the crd or pdb file and see where the bonds are.
Finally, have you considered modelling your second ligand with GLYCAM?
________________________________________
From: Shreeramesh [shreeramesh.gmail.com]
Sent: 20 February 2015 12:33
To: AMBER Mailing List
Subject: Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms
Dears Sir,
I attached the "lig.mol2: file which contains two chlorine atom. While
running tleap "lig.mol2" was combined with another ligand "lig2.mol2".
After the preparation of complex (lig. mol2 and lig2.mol2), the chlorine
atoms are converted into carbon and the bonds between chlorine and carbon
are broken
I did not find the chlorine atoms in the text file of complex:
"com_solvated.pdb"
I checked with different tools for visualization, the problems remains the
same
I also attached the files of (i) lig.mol2 (ii) lig2.mol2 (iii)
com_solvated.pdb (complex: lig.mol2 and lig2.mol2) and (iv) the script for
tleap (tleap.all) for your kind attention
Can you please suggest me why the chlorine atoms are not intact after the
preparation of complex using tleap
Thanks & regards
*Ramesh M*
Email: shreeramesh.gmail.com
Mobile: 91 + (0) 9646469938 27+ (0) 844556164
On Fri, Feb 20, 2015 at 3:39 AM, <hannes.loeffler.stfc.ac.uk> wrote:
> It is rather irrelevant what a certain visualisation programs shows.
> Perhaps it does that because it simply considers the distance between the
> atoms too large. Also, your PDB doesn't contain connectivity information.
>
> What is important, however, is that the prmtop file has all force field
> terms defined? Have you checked that this is true. You have mentioned
> incomplete coordinates...
>
> ________________________________________
> From: Shreeramesh [shreeramesh.gmail.com]
> Sent: 20 February 2015 11:23
> To: AMBER Mailing List
> Subject: Re: [AMBER] Error while running tleap for the ligand containing
> two chlorine atoms
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Feb 20 2015 - 05:30:02 PST
