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*
*======================================*
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Received on Fri Jun 09 2017 - 05:00:02 PDT
