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
Received on Fri Jun 16 2017 - 00:00:02 PDT
