Respected Amber community,
I am trying to make a bond between Threonine and Mannose using Tleap. Here is my input file,
source /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
source /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/oldff/leaprc.ff14SB
source /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.protein.ff14SB
source /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.gaff
list
glyprot =loadpdb thr_man_tutorial.pdb
bond glyprot.2.OG1 glyprot.1.C1
savepdb glyprot man_thr_corr_amber.pdb
saveamberparm glyprot man_thr-tutorial.top man_thr-tutorial.crd
quit
This is the error I am getting:
/home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
Converting C-terminal residue name to PDB format: COLT -> OLT
Checking Unit.
/home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
There is a bond of 6.323369 angstroms between:
/home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
The unperturbed charge of the unit (-1.194000) is not integral.
/home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
The unperturbed charge of the unit (-1.194000) is not zero.
FATAL: Atom .R<AMA 1>.A<C1 1> does not have a type.
FATAL: Atom .R<AMA 1>.A<H1 2> does not have a type.
FATAL: Atom .R<AMA 1>.A<C5 3> does not have a type.
FATAL: Atom .R<AMA 1>.A<H5 4> does not have a type.
FATAL: Atom .R<AMA 1>.A<O5 5> does not have a type.
FATAL: Atom .R<AMA 1>.A<C2 6> does not have a type.
FATAL: Atom .R<AMA 1>.A<H2 7> does not have a type.
FATAL: Atom .R<AMA 1>.A<O2 8> does not have a type.
FATAL: Atom .R<AMA 1>.A<HO2 9> does not have a type.
FATAL: Atom .R<AMA 1>.A<C3 10> does not have a type.
FATAL: Atom .R<AMA 1>.A<H3 11> does not have a type.
FATAL: Atom .R<AMA 1>.A<O3 12> does not have a type.
FATAL: Atom .R<AMA 1>.A<HO3 13> does not have a type.
FATAL: Atom .R<AMA 1>.A<C4 14> does not have a type.
FATAL: Atom .R<AMA 1>.A<H4 15> does not have a type.
FATAL: Atom .R<AMA 1>.A<O4 16> does not have a type.
FATAL: Atom .R<AMA 1>.A<HO4 17> does not have a type.
FATAL: Atom .R<AMA 1>.A<C6 18> does not have a type.
FATAL: Atom .R<AMA 1>.A<H61 19> does not have a type.
FATAL: Atom .R<AMA 1>.A<H62 20> does not have a type.
FATAL: Atom .R<AMA 1>.A<O6 21> does not have a type.
FATAL: Atom .R<AMA 1>.A<HO6 22> does not have a type.
FATAL: Atom .R<COLT 2>.A<HN 15> does not have a type.
FATAL: Atom .R<COLT 2>.A<HG1 16> does not have a type.
FATAL: Atom .R<COLT 2>.A<OT1 17> does not have a type.
FATAL: Atom .R<COLT 2>.A<OT2 18> does not have a type.
/home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Fatal Error!
Failed to generate parameters
Exiting LEaP: Errors = 1; Warnings = 6; Notes = 1.
If any one can suggest the solution that wil be very helpful.
Thanking You,
BILASH MAITY
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Received on Fri Dec 29 2023 - 07:30:02 PST
