I am running tleap for my 343 long chain amino acids. I can not generate any files. Please let me know what commands to use.
Command i am using : /export/home/msoliman/bin/amber10/exe/tleap
leaprc files:
source leaprc.ff99sbchitinase3 = sequence {met pro ser phe lys ser val val ser ser leu pro val ile leu thr ala leu pro ser val gln ala gly leu asp leu ser ser thr ser asn val val val tyr trp gly gln asn ser ala ala ala ser gly gly gly pro ser gln gln pro leu ala thr tyr cys glu asp pro asn ile asp thr leu val met ala phe met thr arg ile asn gly ala gly gly val pro glu ile asn leu ala asn ile gly asp ser cys gly thr phe asp gly thr asn leu lys asp cys pro gln val gly glu asp ile lys lys cys gln ser leu gly lys thr ile leu leu ser ile gly gly ala thr tyr thr glu gly gly phe gln ser ala glu ala ala glu ala gly ala arg met val trp glu thr phe gly pro val thr asn gly asp ala leu arg pro phe gly asp ala val val asp gly phe asp leu asp phe glu ala thr val ser asn met val pro phe ala asn thr leu arg ser leu met asp ser asp ser ser lys gln tyr phe leu thr ala ala pro gln cys pro phe pro asp ala ala asn lys glu met leu asp gly ala val ser phe asp ala ile trp val gln phe tyr asn asn tyr cys gly val asn ser tyr pro asp asn phe asn phe asn thr trp asp asp trp ala gln asn thr ser lys asn lys asn val lys val leu val gly val pro ala asn thr gly ala ala gly ser gly tyr leu pro val asp gln leu ala pro val ile glu his ala arg thr phe pro ser phe gly gly val met met trp asp ala ser gln ala tyr ala asn asp gly phe leu ser gly ile lys ser ile leu gly ser val ile ser arg val lys arg met phe phe arg arg asp phe trp}
saveamberparm chitinase chitinase.prmtop chitinase.prmcrd
/export/home/msoliman/bin/amber10/exe/tleap
source leaprc.ff99SB (uppercase SB)
x= loadpdb test.pdb
saveamberparm x test.prmtop test.inpcrd
Best,
I am now using this leaprc file to load my PDB.
The file contained 15 atoms not in residue templates
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage: saveAmberParm
The Error shows:
The file contained 15 atoms not in residue templates
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage: saveAmberParm
Dear friend
I received your PDB file. Change CD atom type in ILE residues to CD1.
leap can't recognize CD in ILE residue template.
Best
I am now using this leaprc files.
source leaprc.ff99SB
loadpdb chitinase3.pdb
saveamberparm x chitinase3.prmtop chitinase3.inpcrd
command I'm using: /export/home/msoliman/bin/amber10/exe/tleap
please find the corrected PDb attached. Same problem
source leaprc.ff99SB
x=loadpdb chitinase3.pdb
saveamberparm x chitinase3.prmtop chitinase3.inpcrd
Thank You @Hamed Haghshenas, Now I generated my files.
source leaprc.ff99SB
x=loadpdb ABC.pdb
saveamberparm x ABC.prmtop ABC.inpcrd
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