On Tue, 2014-04-29 at 16:17 +0530, MOHD HOMAIDUR RAHMAN wrote:
> 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 ...............
>
> #########################################################
> 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
> ##########################################################
>
> The input leap in command.
>
> ##########################################################
> 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.........
Isolated zwitterionic amino acids are not included in the standard
fragment libraries included with Amber. There are C-terminal and
N-terminal residues (so you can make a zwitterionic dipeptide), but if
you want a zwitterionic amino acid you will need to parametrize a new
residue using something like antechamber or R.E.D.
(
http://q4md-forcefieldtools.org/)
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 29 2014 - 04:30:02 PDT
