AMBER Archive (2008)

Subject: Re: AMBER: missing gaff parameters

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Mar 04 2008 - 08:53:39 CST

You may run parmchk to find the missing parameters and load the generated
frcmod file to leap to generate topologies.

Best

Junmei

On Tue, Mar 4, 2008 at 2:46 AM, Samuele Giani <sgiani_at_pci.unizh.ch> wrote:

> 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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