Dear Sir,
The input file for ligand 1 and ligand 2 are named as lig.mol2 and
lig2.mol2 (In this, the bond between chlorine and carbon are intact)
After running the antichamber the out files are named as LIG.mol2 and
LIG2.mol2 respectively for lig.mol2 and lig2.mol2 using the following
command
command: ~/amber12/bin/antechamber -i lig.mol2 -fi mol2 -o LIG.mol2 -fo
mol2 -j 4 -at gaff -c AM1-BCC -nc 0
~/amber12/bin/parmchk -i LIG.mol2 -f mol2 -o LIG.frcmod
~/amber12/bin/antechamber -i lig2.mol2 -fi mol2 -o
LIG2.mol2 -fo mol2 -j 4 -at gaff -c AM1-BCC -nc 0
~/amber12/bin/parmchk -i LIG2.mol2 -f mol2 -o LIG2.frcmod
Then tleap was run using the tleap script enclosed in attachment for
combining both ligands
After running tleap, "com_solvated.pdb" file was generated, in this, the
bond between carbon and chlorine is missing with the following error message
In other visualization program, the atoms are changed to carbon though
there are chlorine in text file
I also attached frcmod file and com_solvated.pdb for your kind attention
and request you to kindly help me in this regard
Warning in tleap:
hecking 'LIG'....
Warning: Close contact of 1.435025 angstroms between .R<CLM 1>.A<C5 1> and
.R<CLM 1>.A<O5 13>
Warning: Close contact of 1.487896 angstroms between .R<CLM 1>.A<C5 1> and
.R<CLM 1>.A<C6 15>
Warning: Close contact of 1.090127 angstroms between .R<CLM 1>.A<C5 1> and
.R<CLM 1>.A<HC 24>
Warning: Close contact of 1.455269 angstroms between .R<CLM 1>.A<C3 2> and
.R<CLM 1>.A<N2 3>
Warning: Close contact of 1.089962 angstroms between .R<CLM 1>.A<C3 2> and
.R<CLM 1>.A<HC1 25>
Warning: Close contact of 1.334920 angstroms between .R<CLM 1>.A<N2 3> and
.R<CLM 1>.A<C2 4>
Warning: Close contact of 1.010223 angstroms between .R<CLM 1>.A<N2 3> and
.R<CLM 1>.A<H2 6>
Warning: Close contact of 1.224365 angstroms between .R<CLM 1>.A<C2 4> and
.R<CLM 1>.A<O2 5>
Warning: Close contact of 1.089843 angstroms between .R<CLM 1>.A<C1 7> and
.R<CLM 1>.A<HC2 26>
Warning: Close contact of 1.435578 angstroms between .R<CLM 1>.A<C4 10> and
.R<CLM 1>.A<O4 11>
Warning: Close contact of 1.089801 angstroms between .R<CLM 1>.A<C4 10> and
.R<CLM 1>.A<HC3 27>
Warning: Close contact of 1.090034 angstroms between .R<CLM 1>.A<C4 10> and
.R<CLM 1>.A<HC4 28>
Warning: Close contact of 0.959882 angstroms between .R<CLM 1>.A<O4 11> and
.R<CLM 1>.A<HO4 12>
Warning: Close contact of 0.959257 angstroms between .R<CLM 1>.A<O5 13> and
.R<CLM 1>.A<HO5 14>
Warning: Close contact of 1.399501 angstroms between .R<CLM 1>.A<C6 15> and
.R<CLM 1>.A<C7 16>
Warning: Close contact of 1.401859 angstroms between .R<CLM 1>.A<C6 15> and
.R<CLM 1>.A<C11 20>
Warning: Close contact of 1.393831 angstroms between .R<CLM 1>.A<C7 16> and
.R<CLM 1>.A<C8 17>
Warning: Close contact of 1.080099 angstroms between .R<CLM 1>.A<C7 16> and
.R<CLM 1>.A<HC5 29>
Warning: Close contact of 1.400191 angstroms between .R<CLM 1>.A<C8 17> and
.R<CLM 1>.A<C9 18>
Warning: Close contact of 1.080357 angstroms between .R<CLM 1>.A<C8 17> and
.R<CLM 1>.A<HC6 30>
Warning: Close contact of 1.398285 angstroms between .R<CLM 1>.A<C9 18> and
.R<CLM 1>.A<C10 19>
Warning: Close contact of 1.403089 angstroms between .R<CLM 1>.A<C9 18> and
.R<CLM 1>.A<N9 21>
Warning: Close contact of 1.392444 angstroms between .R<CLM 1>.A<C10 19>
and .R<CLM 1>.A<C11 20>
Warning: Close contact of 1.080332 angstroms between .R<CLM 1>.A<C10 19>
and .R<CLM 1>.A<HC7 31>
Warning: Close contact of 1.080200 angstroms between .R<CLM 1>.A<C11 20>
and .R<CLM 1>.A<HC8 32>
Warning: Close contact of 1.229750 angstroms between .R<CLM 1>.A<N9 21> and
.R<CLM 1>.A<O9A 22>
Warning: Close contact of 1.226173 angstroms between .R<CLM 1>.A<N9 21> and
.R<CLM 1>.A<O9B 23>
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
Thanks & regards
*Dr. Ramesh M*
Email: shreeramesh.gmail.com
Mobile: 91 + (0) 9646469938 27+ (0) 844556164
On Sat, Feb 21, 2015 at 7:29 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
>
>
>
>
> On Fri, Feb 20, 2015 at 7:48 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>>
>> > On Feb 20, 2015, at 10:40 AM, David A Case <case.biomaps.rutgers.edu>
>> wrote:
>> >
>> > On Fri, Feb 20, 2015, Jason Swails wrote:
>> >>
>> >> In the OP's defense, if he is using Mac OS X, his filesystem is likely
>> >> case-insensitive, so this should work.
>> >
>> > It won't work: He(she) loaded a mol2 file with Tripos atom types, then
>> > did "saveamberparm". Hard to beleive that this did not emit all kinds
>> of
>> > fatal errors....
>>
>> Oh, of course; antechamber would write out a mol2 with gaff atom types.
>>
>> Thanks,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat Feb 21 2015 - 08:00:03 PST
