Dear Amber user
I want to do MD of amino acid in water mixture. For that I pack the few
molecules of water and alanine in a box with the help of packmol. From pack
pdb, I am trying to generate topology and crd file.
Here alanine have both positive and negative charge (zwitter ionic form).
The single input alanine pdb is ...............
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ATOM 1 N ALA 0 -2.755 4.704 0.161 1.00
ATOM 2 CA ALA 0 -1.566 4.476 -0.658 1.00
ATOM 3 C ALA 0 -1.543 5.723 -1.510 1.00
ATOM 4 O ALA 0 -2.672 6.237 -1.684 1.00
ATOM 5 CB ALA 0 -1.693 3.225 -1.530 1.00
ATOM 6 OXT ALA 0 -0.442 6.153 -1.884 1.00
ATOM 7 H1 ALA 0 -3.359 5.161 -0.526 1.00
ATOM 8 H2 ALA 0 -3.152 3.873 0.554 1.00
ATOM 9 HA ALA 0 -0.672 4.415 -0.036 1.00
ATOM 10 HB1 ALA 0 -1.757 2.334 -0.906 1.00
ATOM 11 HB2 ALA 0 -2.579 3.296 -2.162 1.00
ATOM 12 HB3 ALA 0 -0.812 3.150 -2.170 1.00
ATOM 13 H3 ALA 0 -2.528 5.424 0.824 1.00
END
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The input leap in command.
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source leaprc.ff99bsc0
MY_ALANINE = loadpdb box.pdb
set MY_ALANINE box {34.5 34.5 34.5 }
check MY_ALANINE
charge MY_ALANINE
addions MY_ALANINE Na+ 0
addions MY_ALANINE Cl- 0
saveAmberParm MY_ALANINE ala_10_leap.top ala_10_leap.crd
savepdb MY_ALANINE ala_10_leap.pdb
quit
###########################################################
After running the leap the generated pdb contain two hydrogen less than the
original pdb. this message also given in log file, that is the leap
converting it to C_terminal alanine but we need alanine amino acid.
Leap log file.......
##########################
loadAmberParam = ala-final.frc
> ACHE = loadpdb box.pdb
Loading PDB file: ./box.pdb
Enter zPdbReadScan from call depth 0.
-- residue 1: duplicate [ H] atoms (total 3)
-- residue 2: duplicate [ H] atoms (total 3)
-- residue 3: duplicate [ H] atoms (total 3)
-- residue 4: duplicate [ H] atoms (total 3)
-- residue 5: duplicate [ H] atoms (total 3)
-- residue 6: duplicate [ H] atoms (total 3)
-- residue 7: duplicate [ H] atoms (total 3)
-- residue 8: duplicate [ H] atoms (total 3)
-- residue 9: duplicate [ H] atoms (total 3)
-- residue 10: duplicate [ H] atoms (total 3)
-- residue 11: duplicate [ H] atoms (total 3)
-- residue 12: duplicate [ H] atoms (total 3)
-- residue 13: duplicate [ H] atoms (total 3)
........
.......
.........
Mapped residue ALA, term: Terminal/last, seq. number: 0 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 1 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 2 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 3 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 4 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 5 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 6 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 7 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 8 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 9 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 10 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 11 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 12 to: CALA.
Mapped residue ALA, term: Terminal/last, seq. number: 13 to: CALA.
..................
..................
...................
(Residue 60: WAT, Terminal/last, was not found in name map.)
(Residue 61: WAT, Terminal/last, was not found in name map.)
(Residue 62: WAT, Terminal/last, was not found in name map.)
(Residue 63: WAT, Terminal/last, was not found in name map.)
(Residue 64: WAT, Terminal/last, was not found in name map.)
(Residue 65: WAT, Terminal/last, was not found in name map.)
(Residue 66: WAT, Terminal/last, was not found in name map.)
(Residue 67: WAT, Terminal/last, was not found in name map.)
...................
...................
...................
Writing pdb file: ala_10_leap.pdb
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
Converting C-terminal residue name to PDB format: CALA -> ALA
> quit
##########################
Could anyone suggest me how the generate crd and top from leap for charge
amino acid.........
Thank you in advanced
Regard
Rahman
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Received on Tue Apr 29 2014 - 04:00:02 PDT
