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*
*======================================*
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Fri Jun 09 2017 - 05:30:04 PDT
