AMBER Archive (2008)

Subject: AMBER: missing gaff parameters

From: Samuele Giani (sgiani_at_pci.unizh.ch)
Date: Tue Mar 04 2008 - 02:46:38 CST

Dear All!

I'm trying to build a topology file for an organic molecule using gaff.
My problem arises from the fact that some parameters are missing: what
I've tried to do is to look into the file gaff.dat to see if I could
generate the values with something else mimicking the types but I've got
no chance. Without going for a complete reparametrization, could
somebody be so kind to help me suggesting the parameter to use?

Thank you in advance, Samuele

The molecule .lib is in annexe (rm .xxx extension)...

Could not find angle parameter: ca - c3 - n
Could not find angle parameter: n3 - c3 - ca
Could not find angle parameter: ca - ce - nh
Could not find angle parameter: ca - ce - nh
Could not find angle parameter: nh - ce - nh

  ** No torsion terms for ca-ca-ce-nh
  ** No torsion terms for ca-ca-ce-nh
  ** No torsion terms for ca-ce-nh-hn
  ** No torsion terms for ca-ce-nh-hn
  ** No torsion terms for ca-ce-nh-hn
  ** No torsion terms for ca-ce-nh-hn
  ** No torsion terms for nh-ce-ca-ca
  ** No torsion terms for nh-ce-nh-hn
  ** No torsion terms for nh-ce-nh-hn
  ** No torsion terms for hn-nh-ce-nh
  ** No torsion terms for hn-nh-ce-nh
  ** No torsion terms for nh-ce-ca-ca


!!index array str
 "MOL"
!entry.MOL.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
 "C15" "ca" 0 1 131072 1 6 -0.250140
 "C16" "ca" 0 1 131072 2 6 -0.147170
 "H6" "ha" 0 1 131072 3 1 0.159060
 "H5" "ha" 0 1 131072 4 1 0.172070
 "C14" "ca" 0 1 131072 5 6 0.325580
 "F1" "f" 0 1 131072 6 9 -0.204390
 "C13" "ca" 0 1 131072 7 6 -0.250140
 "H4" "ha" 0 1 131072 8 1 0.172070
 "C12" "ca" 0 1 131072 9 6 -0.147170
 "H3" "ha" 0 1 131072 10 1 0.159060
 "C11" "ca" 0 1 131072 11 6 0.037080
 "C10" "c3" 0 1 131072 12 6 -0.159480
 "H1" "h1" 0 1 131072 13 1 0.121300
 "H2" "h1" 0 1 131072 14 1 0.121300
 "N1" "n" 0 1 131072 15 7 -0.004600
 "C3" "c" 0 1 131072 16 6 0.380930
 "O2" "o" 0 1 131072 17 8 -0.446190
 "C2" "c" 0 1 131072 18 6 0.312390
 "O1" "o" 0 1 131072 19 8 -0.460280
 "C1" "c3" 0 1 131072 20 6 0.000210
 "H24" "hc" 0 1 131072 21 1 0.094800
 "C4" "c3" 0 1 131072 22 6 -0.017140
 "H7" "hc" 0 1 131072 23 1 0.069350
 "C6" "c3" 0 1 131072 24 6 -0.007690
 "C9" "c3" 0 1 131072 25 6 0.020780
 "C8" "c3" 0 1 131072 26 6 -0.027220
 "C7" "c3" 0 1 131072 27 6 -0.000540
 "H9" "h1" 0 1 131072 28 1 0.067590
 "H10" "h1" 0 1 131072 29 1 0.067590
 "H11" "hc" 0 1 131072 30 1 0.033990
 "H12" "hc" 0 1 131072 31 1 0.033990
 "H13" "hc" 0 1 131072 32 1 0.023750
 "H14" "hc" 0 1 131072 33 1 0.023750
 "H8" "h1" 0 1 131072 34 1 0.117890
 "N2" "n3" 0 1 131072 35 7 -0.351570
 "C5" "c3" 0 1 131072 36 6 -0.046800
 "H15" "h1" 0 1 131072 37 1 0.119870
 "C17" "ca" 0 1 131072 38 6 0.002960
 "C18" "ca" 0 1 131072 39 6 -0.057910
 "H16" "ha" 0 1 131072 40 1 0.140540
 "C19" "ca" 0 1 131072 41 6 -0.155640
 "H17" "ha" 0 1 131072 42 1 0.144350
 "C20" "ca" 0 1 131072 43 6 -0.048940
 "C23" "ce" 0 1 131072 44 6 0.672030
 "N3" "nh" 0 1 131072 45 7 -0.831990
 "H22" "hn" 0 1 131072 46 1 0.445340
 "H23" "hn" 0 1 131072 47 1 0.445340
 "N4" "nh" 0 1 131072 48 7 -0.831990
 "H20" "hn" 0 1 131072 49 1 0.445340
 "H21" "hn" 0 1 131072 50 1 0.445340
 "C21" "ca" 0 1 131072 51 6 -0.155640
 "H18" "ha" 0 1 131072 52 1 0.144350
 "C22" "ca" 0 1 131072 53 6 -0.057910
 "H19" "ha" 0 1 131072 54 1 0.140540
!entry.MOL.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
 "C15" "ca" 0 -1 0.0
 "C16" "ca" 0 -1 0.0
 "H6" "ha" 0 -1 0.0
 "H5" "ha" 0 -1 0.0
 "C14" "ca" 0 -1 0.0
 "F1" "f" 0 -1 0.0
 "C13" "ca" 0 -1 0.0
 "H4" "ha" 0 -1 0.0
 "C12" "ca" 0 -1 0.0
 "H3" "ha" 0 -1 0.0
 "C11" "ca" 0 -1 0.0
 "C10" "c3" 0 -1 0.0
 "H1" "h1" 0 -1 0.0
 "H2" "h1" 0 -1 0.0
 "N1" "n" 0 -1 0.0
 "C3" "c" 0 -1 0.0
 "O2" "o" 0 -1 0.0
 "C2" "c" 0 -1 0.0
 "O1" "o" 0 -1 0.0
 "C1" "c3" 0 -1 0.0
 "H24" "hc" 0 -1 0.0
 "C4" "c3" 0 -1 0.0
 "H7" "hc" 0 -1 0.0
 "C6" "c3" 0 -1 0.0
 "C9" "c3" 0 -1 0.0
 "C8" "c3" 0 -1 0.0
 "C7" "c3" 0 -1 0.0
 "H9" "h1" 0 -1 0.0
 "H10" "h1" 0 -1 0.0
 "H11" "hc" 0 -1 0.0
 "H12" "hc" 0 -1 0.0
 "H13" "hc" 0 -1 0.0
 "H14" "hc" 0 -1 0.0
 "H8" "h1" 0 -1 0.0
 "N2" "n3" 0 -1 0.0
 "C5" "c3" 0 -1 0.0
 "H15" "h1" 0 -1 0.0
 "C17" "ca" 0 -1 0.0
 "C18" "ca" 0 -1 0.0
 "H16" "ha" 0 -1 0.0
 "C19" "ca" 0 -1 0.0
 "H17" "ha" 0 -1 0.0
 "C20" "ca" 0 -1 0.0
 "C23" "ce" 0 -1 0.0
 "N3" "nh" 0 -1 0.0
 "H22" "hn" 0 -1 0.0
 "H23" "hn" 0 -1 0.0
 "N4" "nh" 0 -1 0.0
 "H20" "hn" 0 -1 0.0
 "H21" "hn" 0 -1 0.0
 "C21" "ca" 0 -1 0.0
 "H18" "ha" 0 -1 0.0
 "C22" "ca" 0 -1 0.0
 "H19" "ha" 0 -1 0.0
!entry.MOL.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.MOL.unit.childsequence single int
 2
!entry.MOL.unit.connect array int
 1
 53
!entry.MOL.unit.connectivity table int atom1x int atom2x int flags
 1 2 1
 1 4 1
 1 5 1
 2 3 1
 2 11 1
 5 6 1
 5 7 1
 7 8 1
 7 9 1
 9 10 1
 9 11 1
 11 12 1
 12 13 1
 12 14 1
 12 15 1
 15 16 1
 15 18 1
 16 17 1
 16 22 1
 18 19 1
 18 20 1
 20 21 1
 20 22 1
 20 36 1
 22 23 1
 22 24 1
 24 25 1
 24 34 1
 24 35 1
 25 26 1
 25 32 1
 25 33 1
 26 27 1
 26 30 1
 26 31 1
 27 28 1
 27 29 1
 27 35 1
 35 36 1
 36 37 1
 36 38 1
 38 39 1
 38 53 1
 39 40 1
 39 41 1
 41 42 1
 41 43 1
 43 44 1
 43 51 1
 44 45 1
 44 48 1
 45 46 1
 45 47 1
 48 49 1
 48 50 1
 51 52 1
 51 53 1
 53 54 1
!entry.MOL.unit.hierarchy table str abovetype int abovex str belowtype int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
 "R" 1 "A" 2
 "R" 1 "A" 3
 "R" 1 "A" 4
 "R" 1 "A" 5
 "R" 1 "A" 6
 "R" 1 "A" 7
 "R" 1 "A" 8
 "R" 1 "A" 9
 "R" 1 "A" 10
 "R" 1 "A" 11
 "R" 1 "A" 12
 "R" 1 "A" 13
 "R" 1 "A" 14
 "R" 1 "A" 15
 "R" 1 "A" 16
 "R" 1 "A" 17
 "R" 1 "A" 18
 "R" 1 "A" 19
 "R" 1 "A" 20
 "R" 1 "A" 21
 "R" 1 "A" 22
 "R" 1 "A" 23
 "R" 1 "A" 24
 "R" 1 "A" 25
 "R" 1 "A" 26
 "R" 1 "A" 27
 "R" 1 "A" 28
 "R" 1 "A" 29
 "R" 1 "A" 30
 "R" 1 "A" 31
 "R" 1 "A" 32
 "R" 1 "A" 33
 "R" 1 "A" 34
 "R" 1 "A" 35
 "R" 1 "A" 36
 "R" 1 "A" 37
 "R" 1 "A" 38
 "R" 1 "A" 39
 "R" 1 "A" 40
 "R" 1 "A" 41
 "R" 1 "A" 42
 "R" 1 "A" 43
 "R" 1 "A" 44
 "R" 1 "A" 45
 "R" 1 "A" 46
 "R" 1 "A" 47
 "R" 1 "A" 48
 "R" 1 "A" 49
 "R" 1 "A" 50
 "R" 1 "A" 51
 "R" 1 "A" 52
 "R" 1 "A" 53
 "R" 1 "A" 54
!entry.MOL.unit.name single str
 "MOL"
!entry.MOL.unit.positions table dbl x dbl y dbl z
 3.536914 1.422858 -1.933042E-06
 2.620976 2.292419 -0.551187
 1.636679 1.929569 -0.816182
 3.269773 0.387027 0.169057
 4.794792 1.883131 0.363914
 5.673428 1.014780 0.900918
 5.148256 3.202640 0.147931
 6.132923 3.560625 0.426019
 4.219523 4.065986 -0.409126
 4.484493 5.101147 -0.566073
 2.941502 3.630635 -0.760062
 1.945608 4.586827 -1.354117
 2.481102 5.413929 -1.827190
 1.372550 4.078735 -2.131116
 1.038347 5.120300 -0.340803
 1.177801 6.487799 0.142259
 2.196413 7.073556 -0.018721
 -0.094657 4.533125 0.071274
 -0.402749 3.464216 -0.342829
 -0.851089 5.416501 1.017032
 -0.715497 5.111777 2.060000
 -0.197530 6.774930 0.779951
 -0.073458 7.294259 1.737093
 -1.131274 7.575365 -0.113261
 -1.784661 8.819323 0.463813
 -3.117353 8.865820 -0.271919
 -3.488645 7.431376 -0.601826
 -4.276933 7.079950 0.067176
 -3.841436 7.355732 -1.632496
 -3.883289 9.323470 0.354178
 -3.021471 9.450978 -1.188903
 -1.936464 8.723059 1.540917
 -1.189254 9.710531 0.254761
 -0.610942 7.854256 -1.039046
 -2.241324 6.658480 -0.429149
 -2.308527 5.708187 0.706082
 -2.716459 6.243372 1.574971
 -3.185408 4.532453 0.438104
 -3.468598 4.074915 -0.834840
 -3.038700 4.558519 -1.699545
 -4.283342 2.961624 -1.012760
 -4.486673 2.633382 -2.020308
 -4.859128 2.314498 0.074346
 -5.749190 1.135474 -0.161681
 -6.232823 0.428583 0.845339
 -6.021232 0.678024 1.792446
 -6.815186 -0.369298 0.671420
 -6.080390 0.718934 -1.390388
 -5.751260 1.202651 -2.202602
 -6.667131 -0.082488 -1.506397
 -4.578983 2.768923 1.336057
 -5.002216 2.290960 2.208402
 -3.752335 3.873084 1.515953
 -3.545868 4.224593 2.519298
!entry.MOL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
 1 53 0 0 0 0
!entry.MOL.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
 "MOL" 1 55 1 "?" 0
!entry.MOL.unit.residuesPdbSequenceNumber array int
 0
!entry.MOL.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.MOL.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
 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
 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
 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

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