Sure the commands are:
*antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2antechamber
-i lig.pdb -fi pdb -o lig.prepin -fo prepi *
*parmchk -i lig.mol2 -f mol2 -o lig.frcmod*
Sir the pdb file of ligand is attached herewith plz have a look on it.
On Fri, Jun 16, 2017 at 2:46 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> OK.
>
> Can you share your pdb file and the antechamber commands you used?
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>
>
> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> in/elvisadrianmartis/>
>
>
>
>
>
> ________________________________
> From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
> Sent: 16 June 2017 13:00:55
> To: AMBER Mailing List
> Subject: Re: [AMBER] Regarding empty lig.frcmod file
>
> Sir this problem is because of incomplete protonation state of molecule. I
> have added the hydrogen bonds in lig.pdb alone by using autodock tools and
> then used in antechamber by using above command to generate the lig.mol2.
> And it is formed without any hindrance.
>
> On Fri, Jun 16, 2017 at 12:25 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Hi,
> >
> > First of all how did you build the parameters for this molecules??
> >
> > Because when I tried to use antechamber to build parameters using bcc
> > charges, antechamber crashed using following error
> >
> > (command used: antechamber -i lig.mol2 -fi mol2 -o lig_ant.mol2 -fo mol2
> > -s 2 -c bcc)
> >
> > error
> >
> > Welcome to antechamber: molecular input file processor.
> >
> > Info: Finished reading file (lig.mol2).
> > acdoctor mode is on: check and diagnosis problems in the input file.
> > -- Check Format for mol2 File --
> > Status: pass
> > -- Check Unusual Elements --
> > Status: pass
> > -- Check Open Valences --
> > Status: pass
> > -- Check Geometry --
> > for those bonded
> > for those not bonded
> > Status: pass
> > -- Check Weird Bonds --
> > /home/martis/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
> > Weird atomic valence (3) for atom (ID: 17, Name: C4).
> > Possible open valence.
> >
> >
> > This indicates your molecule has unfilled valencies, particularly look at
> > C4 atom. Check how you intended to build this molecule and how it is in
> the
> > lig.mol2 file.
> >
> > Best Regards
> >
> > [photo]
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry)
> > at Bombay College of Pharmacy
> >
> >
> > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> >
> >
> > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > in/elvisadrianmartis/>
> >
> >
> >
> >
> >
> > ________________________________
> > From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
> > Sent: 15 June 2017 23:05:51
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Regarding empty lig.frcmod file
> >
> > Respected Sir,
> >
> > I have tried to load the edited file which you have
> > send it. But the problem is same here. Same fatel error massege is
> > generated.
> >
> >
> >
> >
> > *> a=loadmol2 lig.mol2Loading Mol2 file: ./lig.mol2Reading MOLECULE named
> > LIGFatal Error: last line read: 2 HC1 12.8970 60.2130
> > 31.5730 hc 1 0.098700*
> >
> > Please kindly help me to resolve this problem.
> >
> > Thank you in advance
> >
> >
> > On Fri, Jun 9, 2017 at 6:36 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> > > Hi,
> > >
> > > I tried to fix it.
> > >
> > > added the name of the molecule as "LIG" after the .<TRIPOS>MOLECULE
> line.
> > >
> > > Hope this helps.
> > >
> > >
> > > Best Regards
> > >
> > > [photo]
> > >
> > >
> > >
> > > Elvis Martis
> > > Ph.D. Student (Computational Chemistry)
> > > at Bombay College of Pharmacy
> > >
> > >
> > > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> > > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> > >
> > >
> > > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> > > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > > in/elvisadrianmartis/>
> > >
> > >
> > >
> > >
> > >
> > > ________________________________
> > > From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
> > > Sent: 09 June 2017 18:15:54
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] Regarding empty lig.frcmod file
> > >
> > > Sure Sir the file is attached herewith
> > >
> > > On Fri, Jun 9, 2017 at 5:59 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> > > wrote:
> > >
> > > > Can you send the mol2 file?
> > > >
> > > >
> > > > Best Regards
> > > >
> > > > [photo]
> > > >
> > > >
> > > >
> > > > Elvis Martis
> > > > Ph.D. Student (Computational Chemistry)
> > > > at Bombay College of Pharmacy
> > > >
> > > >
> > > > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > > > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in
> >
> > > > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> > > >
> > > >
> > > > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > > > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> > > > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > > > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > > > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > > > in/elvisadrianmartis/>
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
> > > > Sent: 09 June 2017 17:14:51
> > > > To: AMBER Mailing List
> > > > Subject: Re: [AMBER] Regarding empty lig.frcmod file
> > > >
> > > > Sir how can I rectify this Fatel Error. Please suggest me how can I
> > > resolve
> > > > it
> > > >
> > > > Thank you in advance
> > > >
> > > > On Fri, Jun 9, 2017 at 5:00 PM, Elvis Martis <
> elvis.martis.bcp.edu.in>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > The error says, there is something wrong in your mol2 you have
> > loaded.
> > > > >
> > > > > Check the last line of your mol2 file.
> > > > >
> > > > >
> > > > > Best Regards
> > > > >
> > > > > [photo]
> > > > >
> > > > >
> > > > >
> > > > > Elvis Martis
> > > > > Ph.D. Student (Computational Chemistry)
> > > > > at Bombay College of Pharmacy
> > > > >
> > > > >
> > > > > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > > > > W www.elvismartis.in<https://webapp.wisestamp.com/www.
> elvismartis.in
> > >
> > > > > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> > > > >
> > > > >
> > > > > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > > > > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> > > > > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > > > > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > > > > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > > > > in/elvisadrianmartis/>
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > ________________________________
> > > > > From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
> > > > > Sent: 09 June 2017 12:50:58
> > > > > To: AMBER Mailing List
> > > > > Subject: Re: [AMBER] Regarding empty lig.frcmod file
> > > > >
> > > > > Dear Dr. Martis,
> > > > >
> > > > > I have followed your suggestion but I have faced the following
> > problem
> > > > when
> > > > > I load the input files using *tleap,* which is as follow: Plz help
> me
> > > out
> > > > > to resolve this issue all the input files I have attached in my
> > > previous
> > > > > mail. please suggest me the solution.
> > > > >
> > > > > [vnemaysh.localhost 1DUG]$ tleap
> > > > > -I: Adding /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/prep
> to
> > > > search
> > > > > path.
> > > > > -I: Adding /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib to
> > > > search
> > > > > path.
> > > > > -I: Adding /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/parm
> to
> > > > search
> > > > > path.
> > > > > -I: Adding /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/cmd to
> > > > search
> > > > > path.
> > > > >
> > > > > Welcome to LEaP!
> > > > > (no leaprc in search path)
> > > > > > source leaprc.gaff
> > > > > ----- Source:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/cmd/leaprc.gaff
> > > > > ----- Source of
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/cmd/leaprc.gaff
> > done
> > > > > Log file: ./leap.log
> > > > > Loading parameters:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/parm/gaff.dat
> > > > > Reading title:
> > > > > AMBER General Force Field for organic molecules (Version 1.5,
> January
> > > > 2013)
> > > > > > source leaprc.ff10
> > > > > ----- Source:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/cmd/leaprc.ff10
> > > > > ----- Source of
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/cmd/leaprc.ff10
> > done
> > > > > Log file: ./leap.log
> > > > > Loading parameters:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/parm/parm10.dat
> > > > > Reading title:
> > > > > PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/amino10.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/aminoct10.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/aminont10.lib
> > > > > Could not open file phosphoaa10.lib: not found
> > > > > Could not open database: phosphoaa10.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/nucleic10.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/ions08.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/solvents.lib
> > > > > > source leaprc.ff12SB
> > > > > ----- Source:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/cmd/leaprc.ff12SB
> > > > > ----- Source of
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/cmd/leaprc.ff12SB
> > > done
> > > > > Log file: ./leap.log
> > > > > Loading parameters:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/parm/parm10.dat
> > > > > Reading title:
> > > > > PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> > > > > Loading parameters:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/parm/
> frcmod.ff12SB
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > ff12SB protein backbone and sidechain parameters
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/amino12.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/aminoct12.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/aminont12.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/nucleic12.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/ions08.lib
> > > > > Loading library:
> > > > > /home/vnemaysh/Desktop/Amber_12/amber12/dat/leap/lib/solvents.lib
> > > > > Substituting map 0ALA -> NALA for 0ALA -> NALA
> > > > > Substituting map 1ALA -> CALA for 1ALA -> CALA
> > > > > Substituting map 0ARG -> NARG for 0ARG -> NARG
> > > > > Substituting map 1ARG -> CARG for 1ARG -> CARG
> > > > > Substituting map 0ASN -> NASN for 0ASN -> NASN
> > > > > Substituting map 1ASN -> CASN for 1ASN -> CASN
> > > > > Substituting map 0ASP -> NASP for 0ASP -> NASP
> > > > > Substituting map 1ASP -> CASP for 1ASP -> CASP
> > > > > Substituting map 0CYS -> NCYS for 0CYS -> NCYS
> > > > > Substituting map 1CYS -> CCYS for 1CYS -> CCYS
> > > > > Substituting map 0CYX -> NCYX for 0CYX -> NCYX
> > > > > Substituting map 1CYX -> CCYX for 1CYX -> CCYX
> > > > > Substituting map 0GLN -> NGLN for 0GLN -> NGLN
> > > > > Substituting map 1GLN -> CGLN for 1GLN -> CGLN
> > > > > Substituting map 0GLU -> NGLU for 0GLU -> NGLU
> > > > > Substituting map 1GLU -> CGLU for 1GLU -> CGLU
> > > > > Substituting map 0GLY -> NGLY for 0GLY -> NGLY
> > > > > Substituting map 1GLY -> CGLY for 1GLY -> CGLY
> > > > > Substituting map 0HID -> NHID for 0HID -> NHID
> > > > > Substituting map 1HID -> CHID for 1HID -> CHID
> > > > > Substituting map 0HIE -> NHIE for 0HIE -> NHIE
> > > > > Substituting map 1HIE -> CHIE for 1HIE -> CHIE
> > > > > Substituting map 0HIP -> NHIP for 0HIP -> NHIP
> > > > > Substituting map 1HIP -> CHIP for 1HIP -> CHIP
> > > > > Substituting map 0ILE -> NILE for 0ILE -> NILE
> > > > > Substituting map 1ILE -> CILE for 1ILE -> CILE
> > > > > Substituting map 0LEU -> NLEU for 0LEU -> NLEU
> > > > > Substituting map 1LEU -> CLEU for 1LEU -> CLEU
> > > > > Substituting map 0LYS -> NLYS for 0LYS -> NLYS
> > > > > Substituting map 1LYS -> CLYS for 1LYS -> CLYS
> > > > > Substituting map 0MET -> NMET for 0MET -> NMET
> > > > > Substituting map 1MET -> CMET for 1MET -> CMET
> > > > > Substituting map 0PHE -> NPHE for 0PHE -> NPHE
> > > > > Substituting map 1PHE -> CPHE for 1PHE -> CPHE
> > > > > Substituting map 0PRO -> NPRO for 0PRO -> NPRO
> > > > > Substituting map 1PRO -> CPRO for 1PRO -> CPRO
> > > > > Substituting map 0SER -> NSER for 0SER -> NSER
> > > > > Substituting map 1SER -> CSER for 1SER -> CSER
> > > > > Substituting map 0THR -> NTHR for 0THR -> NTHR
> > > > > Substituting map 1THR -> CTHR for 1THR -> CTHR
> > > > > Substituting map 0TRP -> NTRP for 0TRP -> NTRP
> > > > > Substituting map 1TRP -> CTRP for 1TRP -> CTRP
> > > > > Substituting map 0TYR -> NTYR for 0TYR -> NTYR
> > > > > Substituting map 1TYR -> CTYR for 1TYR -> CTYR
> > > > > Substituting map 0VAL -> NVAL for 0VAL -> NVAL
> > > > > Substituting map 1VAL -> CVAL for 1VAL -> CVAL
> > > > > Substituting map 0HIS -> NHIS for 0HIS -> NHIS
> > > > > Substituting map 1HIS -> CHIS for 1HIS -> CHIS
> > > > > Substituting map 0G -> G5 for 0G -> G5
> > > > > Substituting map 1G -> G3 for 1G -> G3
> > > > > Substituting map 0A -> A5 for 0A -> A5
> > > > > Substituting map 1A -> A3 for 1A -> A3
> > > > > Substituting map 0C -> C5 for 0C -> C5
> > > > > Substituting map 1C -> C3 for 1C -> C3
> > > > > Substituting map 0U -> U5 for 0U -> U5
> > > > > Substituting map 1U -> U3 for 1U -> U3
> > > > > Substituting map 0DG -> DG5 for 0DG -> DG5
> > > > > Substituting map 1DG -> DG3 for 1DG -> DG3
> > > > > Substituting map 0DA -> DA5 for 0DA -> DA5
> > > > > Substituting map 1DA -> DA3 for 1DA -> DA3
> > > > > Substituting map 0DC -> DC5 for 0DC -> DC5
> > > > > Substituting map 1DC -> DC3 for 1DC -> DC3
> > > > > Substituting map 0DT -> DT5 for 0DT -> DT5
> > > > > Substituting map 1DT -> DT3 for 1DT -> DT3
> > > > > Substituting map 0RA5 -> A5 for 0RA5 -> A5
> > > > > Substituting map 1RA3 -> A3 for 1RA3 -> A3
> > > > > Substituting map RA -> A for RA -> A
> > > > > Substituting map 0RC5 -> C5 for 0RC5 -> C5
> > > > > Substituting map 1RC3 -> C3 for 1RC3 -> C3
> > > > > Substituting map RC -> C for RC -> C
> > > > > Substituting map 0RG5 -> G5 for 0RG5 -> G5
> > > > > Substituting map 1RG3 -> G3 for 1RG3 -> G3
> > > > > Substituting map RG -> G for RG -> G
> > > > > Substituting map 0RU5 -> U5 for 0RU5 -> U5
> > > > > Substituting map 1RU3 -> U3 for 1RU3 -> U3
> > > > > Substituting map RU -> U for RU -> U
> > > > > Substituting map 0GUA -> DG5 for 0GUA -> DG5
> > > > > Substituting map 1GUA -> DG3 for 1GUA -> DG3
> > > > > Substituting map GUA -> DG for GUA -> DG
> > > > > Substituting map 0ADE -> DA5 for 0ADE -> DA5
> > > > > Substituting map 1ADE -> DA3 for 1ADE -> DA3
> > > > > Substituting map ADE -> DA for ADE -> DA
> > > > > Substituting map 0CYT -> DC5 for 0CYT -> DC5
> > > > > Substituting map 1CYT -> DC3 for 1CYT -> DC3
> > > > > Substituting map CYT -> DC for CYT -> DC
> > > > > Substituting map 0THY -> DT5 for 0THY -> DT5
> > > > > Substituting map 1THY -> DT3 for 1THY -> DT3
> > > > > Substituting map THY -> DT for THY -> DT
> > > > > Substituting map O5* -> O5' for O5* -> O5'
> > > > > Substituting map C5* -> C5' for C5* -> C5'
> > > > > Substituting map C4* -> C4' for C4* -> C4'
> > > > > Substituting map O4* -> O4' for O4* -> O4'
> > > > > Substituting map C3* -> C3' for C3* -> C3'
> > > > > Substituting map O3* -> O3' for O3* -> O3'
> > > > > Substituting map C2* -> C2' for C2* -> C2'
> > > > > Substituting map O2* -> O2' for O2* -> O2'
> > > > > Substituting map C1* -> C1' for C1* -> C1'
> > > > > Substituting map C5M -> C7 for C5M -> C7
> > > > > Substituting map H1* -> H1' for H1* -> H1'
> > > > > Substituting map H2*1 -> H2' for H2*1 -> H2'
> > > > > Substituting map H2*2 -> H2'' for H2*2 -> H2''
> > > > > Substituting map H2'1 -> H2' for H2'1 -> H2'
> > > > > Substituting map H2'2 -> H2'' for H2'2 -> H2''
> > > > > Substituting map H3* -> H3' for H3* -> H3'
> > > > > Substituting map H4* -> H4' for H4* -> H4'
> > > > > Substituting map H5*1 -> H5' for H5*1 -> H5'
> > > > > Substituting map H5*2 -> H5'' for H5*2 -> H5''
> > > > > Substituting map H5'1 -> H5' for H5'1 -> H5'
> > > > > Substituting map H5'2 -> H5'' for H5'2 -> H5''
> > > > > Substituting map HO'2 -> HO2' for HO'2 -> HO2'
> > > > > Substituting map H5T -> HO5' for H5T -> HO5'
> > > > > Substituting map H3T -> HO3' for H3T -> HO3'
> > > > > Substituting map O1' -> O4' for O1' -> O4'
> > > > > Substituting map OA -> OP1 for OA -> OP1
> > > > > Substituting map OB -> OP2 for OB -> OP2
> > > > > Substituting map O1P -> OP1 for O1P -> OP1
> > > > > Substituting map O2P -> OP2 for O2P -> OP2
> > > > > > list
> > > > > A A3 A5 ACE ALA AN ARG
> > > > > ASH
> > > > > ASN ASP Br- C C3 C5 CALA
> > > > > CARG
> > > > > CASN CASP CCYS CCYX CGLN CGLU CGLY
> > > > > CHCL3BOX
> > > > > CHID CHIE CHIP CHIS CHYP CILE CLEU
> > > > > CLYS
> > > > > CMET CN CPHE CPRO CSER CTHR CTRP
> > > > > CTYR
> > > > > CVAL CYM CYS CYX Cl- Cs+ DA
> > > > > DA3
> > > > > DA5 DAN DC DC3 DC4 DC5 DCN
> > > > > DG
> > > > > DG3 DG5 DGN DT DT3 DT5 DTN
> > > > > F-
> > > > > G G3 G5 GLH GLN GLU GLY
> > > > > GN
> > > > > HID HIE HIP HIS HOH HYP I-
> > > > > ILE
> > > > > K+ LEU LYN LYS Li+ MEOHBOX MET
> > > > > Mg+
> > > > > NALA NARG NASN NASP NCYS NCYX NGLN
> > > > > NGLU
> > > > > NGLY NHE NHID NHIE NHIP NHIS NILE
> > > > > NLEU
> > > > > NLYS NMABOX NME NMET NPHE NPRO NSER
> > > > > NTHR
> > > > > NTRP NTYR NVAL Na+ OHE PHE PL3
> > > > > POL3BOX
> > > > > PRO QSPCFWBOX Rb+ SER SPC SPCBOX
> SPCFWBOX
> > > > > SPF
> > > > > SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX
> > > > > TIP4PEWBOXTIP5PBOX
> > > > > TP3 TP4 TP5 TPF TRP TYR U
> > > > > U3
> > > > > U5 UN VAL WAT frcmod12SBgaff parm10
> > > > > > loadamberprep lig.prepin
> > > > > Loading Prep file: ./lig.prepin
> > > > > > loadamberparams lig.frcmod
> > > > > Loading parameters: ./lig.frcmod
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > remark goes here
> > > > > > a=loadmol2 lig.mol2
> > > > > Loading Mol2 file: ./lig.mol2
> > > > > Reading MOLECULE named 35 34 1 0 0
> > > > >
> > > > > *Fatal Error: last line read: 1 C 12.9060 59.1090
> > > > > 31.7270 c3 1 -0.086400> *
> > > > >
> > > > > Thanking you in advance
> > > > >
> > > > >
> > > > > On Tue, Jun 6, 2017 at 10:02 PM, Elvis Martis <
> > elvis.martis.bcp.edu.in
> > > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > There is nothing wrong in this. GAFF has all the parameters for
> > your
> > > > > > ligand.
> > > > > >
> > > > > > Go ahead and load that in leap and see if you can save the
> > lig.prmtop
> > > > and
> > > > > > lig.inpcrd.
> > > > > >
> > > > > > If yes, then there is no problem at all.
> > > > > >
> > > > > >
> > > > > > Best Regards
> > > > > >
> > > > > > [photo]
> > > > > >
> > > > > >
> > > > > >
> > > > > > Elvis Martis
> > > > > > Ph.D. Student (Computational Chemistry)
> > > > > > at Bombay College of Pharmacy
> > > > > >
> > > > > >
> > > > > > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > > > > > W www.elvismartis.in<https://webapp.wisestamp.com/www.
> > elvismartis.in
> > > >
> > > > > > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> > > > > >
> > > > > >
> > > > > > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > > > > > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-
> wqOlXSGjbmEyga9C8lmU1bs-_
> > > > > > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > > > > > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > > > > > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > > > > > in/elvisadrianmartis/>
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > ________________________________
> > > > > > From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
> > > > > > Sent: 06 June 2017 21:57:45
> > > > > > To: AMBER Mailing List
> > > > > > Subject: [AMBER] Regarding empty lig.frcmod file
> > > > > >
> > > > > > Dear Amber Users,
> > > > > >
> > > > > > I have used antechamber module of AMBER 12 for ligand parameter
> > files
> > > > > > preparation for MD simulation and I have facing the problem in
> the*
> > > > > > lig.frcmod* file generation, which is empty and there is no any
> > > > parameter
> > > > > > for ligand its just showing the following text
> > > > > >
> > > > > > remark goes here
> > > > > > MASS
> > > > > >
> > > > > > BOND
> > > > > >
> > > > > > ANGLE
> > > > > >
> > > > > > DIHE
> > > > > >
> > > > > > IMPROPER
> > > > > >
> > > > > > NONBON
> > > > > >
> > > > > > I think rest of the files are generated successfully. Please
> kindly
> > > > > suggest
> > > > > > me how can I resolve this problem.
> > > > > >
> > > > > > I have attached all the files which I have generated including
> > > > > *lig.frcmod
> > > > > > *for
> > > > > > your reference.
> > > > > >
> > > > > > Thanking you in advance
> > > > > >
> > > > > > Regards....
> > > > > > --
> > > > > > *Vishal Nemaysh, PhD*
> > > > > > *Neuropharmaceutical Chemistry Group,*
> > > > > > *Dr. B. R. Ambedkar Center for Biomedical Research,*
> > > > > > *University of Delhi, Delhi-110007, INDIA*
> > > > > > *Email: vishal.bioinfotech.gmail.com <
> vishal.bioinfotech.gmail.com
> > >*
> > > > > > *LinkedIn: vishalnemaysh.hotmail.com <vishalnemaysh.hotmail.com
> >*
> > > > > > *Mobile: 91+8447581401, 91+9650736653*
> > > > > > *======================================*
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > *Vishal Nemaysh, PhD*
> > > > > *Neuropharmaceutical Chemistry Group,*
> > > > > *Dr. B. R. Ambedkar Center for Biomedical Research,*
> > > > > *University of Delhi, Delhi-110007, INDIA*
> > > > > *Email: vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com
> >*
> > > > > *LinkedIn: vishalnemaysh.hotmail.com <vishalnemaysh.hotmail.com>*
> > > > > *Mobile: 91+8447581401, 91+9650736653*
> > > > > *======================================*
> > > > > _______________________________________________
> > > > > 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
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > *Vishal Nemaysh, PhD*
> > > > *Neuropharmaceutical Chemistry Group,*
> > > > *Dr. B. R. Ambedkar Center for Biomedical Research,*
> > > > *University of Delhi, Delhi-110007, INDIA*
> > > > *Email: vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> > > > *LinkedIn: vishalnemaysh.hotmail.com <vishalnemaysh.hotmail.com>*
> > > > *Mobile: 91+8447581401, 91+9650736653*
> > > > *======================================*
> > > > _______________________________________________
> > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > *Vishal Nemaysh, PhD*
> > > *Neuropharmaceutical Chemistry Group,*
> > > *Dr. B. R. Ambedkar Center for Biomedical Research,*
> > > *University of Delhi, Delhi-110007, INDIA*
> > > *Email: vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> > > *LinkedIn: vishalnemaysh.hotmail.com <vishalnemaysh.hotmail.com>*
> > > *Mobile: 91+8447581401, 91+9650736653*
> > > *======================================*
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> > *Vishal Nemaysh, PhD*
> > *Neuropharmaceutical Chemistry Group,*
> > *Dr. B. R. Ambedkar Center for Biomedical Research,*
> > *University of Delhi, Delhi-110007, INDIA*
> > *Email: vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> > *LinkedIn: vishalnemaysh.hotmail.com <vishalnemaysh.hotmail.com>*
> > *Mobile: 91+8447581401, 91+9650736653*
> > *======================================*
> > _______________________________________________
> > 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
> >
>
>
>
> --
> *Vishal Nemaysh, PhD*
> *Neuropharmaceutical Chemistry Group,*
> *Dr. B. R. Ambedkar Center for Biomedical Research,*
> *University of Delhi, Delhi-110007, INDIA*
> *Email: vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> *LinkedIn: vishalnemaysh.hotmail.com <vishalnemaysh.hotmail.com>*
> *Mobile: 91+8447581401, 91+9650736653*
> *======================================*
> _______________________________________________
> 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
>
--
*Vishal Nemaysh, PhD*
*Neuropharmaceutical Chemistry Group,*
*Dr. B. R. Ambedkar Center for Biomedical Research,*
*University of Delhi, Delhi-110007, INDIA*
*Email: vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
*LinkedIn: vishalnemaysh.hotmail.com <vishalnemaysh.hotmail.com>*
*Mobile: 91+8447581401, 91+9650736653*
*======================================*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 16 2017 - 06:00:05 PDT
