AMBER Archive (2008)

Subject: Re: AMBER: Hydroxyproline in AMBER

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Jul 23 2008 - 11:14:06 CDT

This is our own adaptation from VJ Pande's paper that carlos just
referred to.

Adrian

PS: I had to change the attachment name so filters wil llet it go through.

put them back as hyp.lib

Michael Entz wrote:
> Hello,
>
> Does anyone know of a library file for AMBER that would allow me to us
> hydroxyproline for simulations? I am using AMBER9 and don't see any force
> fields that already include HYP.
>
> Thank you,
>
> --
> Michael William Entz II
> North Carolina State University
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

HEADER TOXIN 23-JUN-04 1TTL
TITLE OMEGA-CONOTOXIN GVIA, A N-TYPE CALCIUM CHANNEL BLOCKER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: OMEGA-CONOTOXIN GVIA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: GVIC
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: CONUS GEOGRAPHUS;
SOURCE 3 ORGANISM_COMMON: GEOGRAPHY CONE;
SOURCE 4 SECRETION: VENOM
KEYWDS DISULFIDE RICH, FOUR LOOP FRAMEWORK, AMIDATED C-TERMINAL
EXPDTA NMR, 20 STRUCTURES
AUTHOR J.MOULD,T.YASUDA,C.I.SCHROEDER,A.M.BEEDLE,C.J.DOERING,
AUTHOR 2 G.W.ZAMPONI,D.J.ADAMS,R.J.LEWIS
REVDAT 2 12-OCT-04 1TTL 1 JRNL
REVDAT 1 13-JUL-04 1TTL 0
JRNL AUTH J.MOULD,T.YASUDA,C.I.SCHROEDER,A.M.BEEDLE,
JRNL AUTH 2 C.J.DOERING,G.W.ZAMPONI,D.J.ADAMS,R.J.LEWIS
JRNL TITL THE ALPHA2DELTA AUXILIARY SUBUNIT REDUCES AFFINITY
JRNL TITL 2 OF OMEGA-CONOTOXINS FOR RECOMBINANT N-TYPE
JRNL TITL 3 (CAV2.2) CALCIUM CHANNELS
JRNL REF J.BIOL.CHEM. V. 279 34705 2004
JRNL REFN ASTM JBCHA3 US ISSN 0021-9258
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 533 DISTANCE RESTRAINTS
REMARK 3 (INCLUDING H-BONDS) AND 31 DIHEDRAL ANGLE RESTRAINTS
REMARK 3 (INCLUDING 16 PHI AND 15 CHI) WERE USED TO CALCULATE THESE
REMARK 3 STRUCTURES.
REMARK 4
REMARK 4 1TTL COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 4
REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY.
REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17)
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB.
REMARK 100 THE RCSB ID CODE IS RCSB022890.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293; 275
REMARK 210 PH : 3.5; 3.5
REMARK 210 IONIC STRENGTH : NULL; NULL
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 2 MM GVIA, DSS; 2 MM GVIA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY,
REMARK 210 E-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 500 MHZ
REMARK 210 SPECTROMETER MODEL : AMX, DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 3.5, X-PLOR 3.851
REMARK 210 METHOD USED : SOLUTION STRUCTURES WERE
REMARK 210 CALCULATED USING TORSION ANGLE
REMARK 210 DYNAMICS/SIMULATED ANNEALING
REMARK 210 PROTOCOLS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR NMR TECHNIQUES.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI
REMARK 500 C TYR A 27 N NH2 A 28 1.31
REMARK 500 O TYR A 27 N NH2 A 28 2.17
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 SER A 9 HYP A 10 2 -143.43
REMARK 500 SER A 9 HYP A 10 4 148.56
REMARK 500 SER A 9 HYP A 10 7 149.98
REMARK 500 SER A 9 HYP A 10 12 -135.16
REMARK 500 SER A 9 HYP A 10 13 149.54
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2CCO RELATED DB: PDB
REMARK 900 STRUCTURE OF THE CALCIUM CHANNEL BLOCKER CONOTOXIN GVIA,
REMARK 900 NMR, 20 STRUCTURES
REMARK 900 RELATED ID: 1OMC RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF OMEGA-CONOTOXIN GVIA USING 2-D NMR
REMARK 900 SPECTROSCOPY AND RELAXATION MATRIX ANALYSIS.
DBREF 1TTL A 1 27 UNP P01522 CXO6_CONGE 46 72
SEQADV 1TTL HYP A 4 UNP P01522 PRO 49 MODIFIED RESIDUE
SEQADV 1TTL HYP A 10 UNP P01522 PRO 55 MODIFIED RESIDUE
SEQADV 1TTL HYP A 21 UNP P01522 PRO 66 MODIFIED RESIDUE
SEQRES 1 A 27 CYS LYS SER HYP GLY SER SER CYS SER HYP THR SER TYR
SEQRES 2 A 27 ASN CYS CYS ARG SER CYS ASN HYP TYR THR LYS ARG CYS
SEQRES 3 A 27 TYR
MODRES 1TTL HYP A 4 PRO 4-HYDROXYPROLINE
MODRES 1TTL HYP A 10 PRO 4-HYDROXYPROLINE
MODRES 1TTL HYP A 21 PRO 4-HYDROXYPROLINE
HET HYP A 4 15
HET HYP A 10 15
HET HYP A 21 15
HET NH2 A 28 3
HETNAM HYP 4-HYDROXYPROLINE
HETNAM NH2 AMINO GROUP
HETSYN HYP HYDROXYPROLINE
FORMUL 1 HYP 3(C5 H9 N O3)
FORMUL 2 NH2 H2 N
SHEET 1 A 2 CYS A 19 ASN A 20 0
SHEET 2 A 2 ARG A 25 CYS A 26 -1 O ARG A 25 N ASN A 20
SSBOND 1 CYS A 1 CYS A 16
SSBOND 2 CYS A 8 CYS A 19
SSBOND 3 CYS A 15 CYS A 26
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
HETATM 46 N HYP A 4 10.349 -0.406 2.137 1.00 0.00 N
HETATM 47 CA HYP A 4 10.618 -1.196 0.921 1.00 0.00 C
HETATM 48 C HYP A 4 11.127 -0.409 -0.304 1.00 0.00 C
HETATM 49 O HYP A 4 10.510 0.551 -0.723 1.00 0.00 O
HETATM 50 CB HYP A 4 9.296 -1.886 0.688 1.00 0.00 C
HETATM 51 CG HYP A 4 8.287 -0.833 1.094 1.00 0.00 C
HETATM 52 CD HYP A 4 9.033 0.224 1.906 1.00 0.00 C
HETATM 53 OD1 HYP A 4 7.273 -1.430 1.889 1.00 0.00 O
HETATM 54 HA HYP A 4 11.344 -1.965 1.123 1.00 0.00 H
HETATM 55 HB2 HYP A 4 9.236 -2.777 1.296 1.00 0.00 H
HETATM 56 HB3 HYP A 4 9.196 -2.181 -0.346 1.00 0.00 H
HETATM 57 HG HYP A 4 7.853 -0.383 0.212 1.00 0.00 H
HETATM 58 HD22 HYP A 4 8.503 0.432 2.818 1.00 0.00 H
HETATM 59 HD23 HYP A 4 9.154 1.149 1.366 1.00 0.00 H
HETATM 60 HD1 HYP A 4 7.682 -1.751 2.697 1.00 0.00 H
END


!!index array str
 "HYP"
!entry.HYP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
 "N" "N" 0 1 131075 1 7 -0.254800
 "CA" "CT" 0 1 131075 2 6 0.004700
 "C" "C" 0 1 131075 3 6 0.589600
 "O" "O" 0 1 131075 4 8 -0.574800
 "CB" "CT" 0 1 131075 5 6 0.020300
 "CG" "CT" 0 1 131075 6 6 0.040000
 "CD" "CT" 0 1 131075 7 6 0.059500
 "OD1" "OH" 0 1 131075 8 8 -0.613400
 "HA" "H1" 0 1 131075 9 1 0.077000
 "HB2" "HC" 0 1 131075 10 1 0.042600
 "HB3" "HC" 0 1 131075 11 1 0.042600
 "HG" "H1" 0 1 131075 12 1 0.041600
 "HD22" "H1" 0 1 131075 13 1 0.070000
 "HD23" "H1" 0 1 131075 14 1 0.070000
 "HD1" "HO" 0 1 131075 15 1 0.385100
!entry.HYP.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
 "N" "N" 0 -1 0.0
 "CA" "CT" 0 -1 0.0
 "C" "C" 0 -1 0.0
 "O" "O" 0 -1 0.0
 "CB" "CT" 0 -1 0.0
 "CG" "CT" 0 -1 0.0
 "CD" "CT" 0 -1 0.0
 "OD1" "OH" 0 -1 0.0
 "HA" "H1" 0 -1 0.0
 "HB2" "HC" 0 -1 0.0
 "HB3" "HC" 0 -1 0.0
 "HG" "H1" 0 -1 0.0
 "HD22" "H1" 0 -1 0.0
 "HD23" "H1" 0 -1 0.0
 "HD1" "HO" 0 -1 0.0
!entry.HYP.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.HYP.unit.childsequence single int
 5
!entry.HYP.unit.connect array int
 1
 3
!entry.HYP.unit.connectivity table int atom1x int atom2x int flags
 8 15 1
 7 13 1
 7 14 1
 6 8 1
 6 12 1
 6 7 1
 5 11 1
 5 10 1
 5 6 1
 3 4 1
 2 3 1
 2 9 1
 2 5 1
 1 2 1
 1 7 1
!entry.HYP.unit.hierarchy table str abovetype int abovex str belowtype int belowx
 "U" 0 "R" 1
 "R" 1 "A" 15
 "R" 1 "A" 14
 "R" 1 "A" 13
 "R" 1 "A" 12
 "R" 1 "A" 11
 "R" 1 "A" 10
 "R" 1 "A" 9
 "R" 1 "A" 8
 "R" 1 "A" 7
 "R" 1 "A" 6
 "R" 1 "A" 5
 "R" 1 "A" 4
 "R" 1 "A" 3
 "R" 1 "A" 2
 "R" 1 "A" 1
!entry.HYP.unit.name single str
 ""
!entry.HYP.unit.positions table dbl x dbl y dbl z
 10.349000 -0.406000 2.137000
 10.618000 -1.196000 0.921000
 11.127000 -0.409000 -0.304000
 10.510000 0.551000 -0.723000
 9.296000 -1.886000 0.688000
 8.287000 -0.833000 1.094000
 9.033000 0.224000 1.906000
 7.273000 -1.430000 1.889000
 11.344000 -1.965000 1.123000
 9.236000 -2.777000 1.296000
 9.196000 -2.181000 -0.346000
 7.853000 -0.383000 0.212000
 8.503000 0.432000 2.818000
 9.154000 1.149000 1.366000
 7.682000 -1.751000 2.697000
!entry.HYP.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
 0 0 0 0 0 0
!entry.HYP.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
 "HYP" 4 17 1 "?" 0
!entry.HYP.unit.residuesPdbSequenceNumber array int
 1
!entry.HYP.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.HYP.unit.velocities table dbl x dbl y dbl z
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0

MASS

BOND

ANGLE

DIHEDRAL
N-CT-CT-OH 1 0. 0.0 -1.
N-CT-CT-OH 1 1.49 0.0 -2.
N-CT-CT-OH 1 0.156 0.0 -3.
N-CT-CT-OH 1 0. 0.0 4.

NONBON
 

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