AMBER Archive (2008)

Subject: Re: AMBER: autodock pdb to obtain parm with tleap

From: Henar Martínez (henar_at_eis.uva.es)
Date: Wed Feb 27 2008 - 04:58:09 CST

David A. Case escribió:
> On Tue, Feb 26, 2008, Henar Martínez wrote:
>
>
>> Anybody know how to transform an autodock pdb file in a pdb one that
>> tleap can use to generate the parm file.
>> The problem is: tleap does not recognize the atom types of the autodock
>> pdb file.
>>
>
> We would need to see at least a little bit of the file to know what you are
> talking about. PDB files do not store atom type information, so it's hard
> to know what the real problem is.
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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>
>
Thank you dac for your answer,
The pdb file is:
> REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.0
> ATOM 1 C1 MOL 371 -10.209 -1.790 7.103 1.00
> 0.00 conf C
> ATOM 2 H11 MOL 371 -9.283 -1.928 6.498 1.00
> 0.00 conf H
> ATOM 3 H12 MOL 371 -10.155 -2.706 7.736 1.00
> 0.00 conf H
> ATOM 4 C5 MOL 371 -10.110 -0.537 7.960 1.00
> 0.00 conf C
> ATOM 5 H5 MOL 371 -10.961 -0.511 8.680 1.00
> 0.00 conf H
> ATOM 6 C3 MOL 371 -10.131 0.718 7.107 1.00
> 0.00 conf C
> ATOM 7 H3 MOL 371 -9.234 0.697 6.445 1.00
> 0.00 conf H
> ATOM 8 C4 MOL 371 -11.381 0.847 6.208 1.00
> 0.00 conf C
> ATOM 9 C2 MOL 371 -11.515 -0.483 5.397 1.00
> 0.00 conf C
> ATOM 10 H2 MOL 371 -10.602 -0.509 4.758 1.00
> 0.00 conf H
> ATOM 11 C15 MOL 371 -12.677 -0.515 4.397 1.00
> 0.00 conf C
> ATOM 12 1H15 MOL 371 -13.656 -0.706 4.895 1.00
> 0.00 conf H
> ATOM 13 2H15 MOL 371 -12.903 0.495 3.981 1.00
> 0.00 conf H
> ATOM 14 C13 MOL 371 -12.378 -1.536 3.302 1.00
> 0.00 conf C
> ATOM 15 1H13 MOL 371 -11.538 -1.181 2.660 1.00
> 0.00 conf H
> ATOM 16 2H13 MOL 371 -13.201 -1.551 2.550 1.00
> 0.00 conf H
> ATOM 17 C6 MOL 371 -11.463 -1.824 6.199 1.00
> 0.00 conf C
> ATOM 18 C10 MOL 371 -11.359 -2.991 5.182 1.00
> 0.00 conf C
> ATOM 19 C12 MOL 371 -10.754 -4.129 5.509 1.00
> 0.00 conf C
> ATOM 20 H12 MOL 371 -10.274 -4.208 6.499 1.00
> 0.00 conf H
> ATOM 21 C16 MOL 371 -10.699 -5.282 4.607 1.00
> 0.00 conf C
> ATOM 22 H16 MOL 371 -10.453 -6.273 5.024 1.00
> 0.00 conf H
> ATOM 23 C11 MOL 371 -12.094 -2.969 3.818 1.00
> 0.00 conf C
> ATOM 24 C17 MOL 371 -11.234 -3.771 2.752 1.00
> 0.00 conf C
> ATOM 25 C19 MOL 371 -9.859 -3.096 2.506 1.00
> 0.00 conf C
> ATOM 26 1H19 MOL 371 -9.326 -3.049 3.484 1.00
> 0.00 conf H
> ATOM 27 2H19 MOL 371 -9.947 -2.100 2.012 1.00
> 0.00 conf H
> ATOM 28 3H19 MOL 371 -9.263 -3.602 1.711 1.00
> 0.00 conf H
> ATOM 29 C25 MOL 371 -11.975 -3.836 1.391 1.00
> 0.00 conf C
> ATOM 30 1H25 MOL 371 -13.077 -3.879 1.552 1.00
> 0.00 conf H
> ATOM 31 2H25 MOL 371 -11.896 -2.859 0.860 1.00
> 0.00 conf H
> ATOM 32 C24 MOL 371 -11.528 -4.977 0.473 1.00
> 0.00 conf C
> ATOM 33 1H24 MOL 371 -10.489 -4.816 0.102 1.00
> 0.00 conf H
> ATOM 34 2H24 MOL 371 -12.068 -4.948 -0.502 1.00
> 0.00 conf H
> ATOM 35 C22 MOL 371 -11.674 -6.349 1.154 1.00
> 0.00 conf C
> ATOM 36 C18 MOL 371 -10.934 -5.175 3.308 1.00
> 0.00 conf C
> ATOM 37 C20 MOL 371 -10.773 -6.402 2.409 1.00
> 0.00 conf C
> ATOM 38 H20 MOL 371 -11.097 -7.287 3.005 1.00
> 0.00 conf H
> ATOM 39 C21 MOL 371 -9.284 -6.622 2.045 1.00
> 0.00 conf C
> ATOM 40 1H21 MOL 371 -8.858 -5.694 1.596 1.00
> 0.00 conf H
> ATOM 41 2H21 MOL 371 -8.669 -6.691 2.973 1.00
> 0.00 conf H
> ATOM 42 C26 MOL 371 -9.001 -7.829 1.132 1.00
> 0.00 conf C
> ATOM 43 C28 MOL 371 -7.520 -7.808 0.727 1.00
> 0.00 conf C
> ATOM 44 1H28 MOL 371 -6.890 -7.910 1.641 1.00
> 0.00 conf H
> ATOM 45 2H28 MOL 371 -7.257 -6.904 0.130 1.00
> 0.00 conf H
> ATOM 46 3H28 MOL 371 -7.280 -8.579 -0.042 1.00
> 0.00 conf H
> ATOM 47 C29 MOL 371 -9.870 -7.688 -0.128 1.00
> 0.00 conf C
> ATOM 48 1H29 MOL 371 -9.704 -8.545 -0.822 1.00
> 0.00 conf H
> ATOM 49 2H29 MOL 371 -9.502 -6.856 -0.772 1.00
> 0.00 conf H
> ATOM 50 C30 MOL 371 -11.358 -7.519 0.181 1.00
> 0.00 conf C
> ATOM 51 1H30 MOL 371 -11.944 -7.413 -0.762 1.00
> 0.00 conf H
> ATOM 52 2H30 MOL 371 -11.789 -8.473 0.564 1.00
> 0.00 conf H
> ATOM 53 C9 MOL 371 -11.111 2.006 5.223 1.00
> 0.00 conf C
> ATOM 54 H91 MOL 371 -11.015 2.954 5.801 1.00
> 0.00 conf H
> ATOM 55 H92 MOL 371 -11.883 2.072 4.421 1.00
> 0.00 conf H
> ATOM 56 H93 MOL 371 -10.227 1.814 4.571 1.00
> 0.00 conf H
> ATOM 57 C7 MOL 371 -12.629 1.237 7.021 1.00
> 0.00 conf C
> ATOM 58 H71 MOL 371 -12.824 0.400 7.732 1.00
> 0.00 conf H
> ATOM 59 H72 MOL 371 -13.509 1.486 6.383 1.00
> 0.00 conf H
> ATOM 60 H73 MOL 371 -12.535 2.228 7.523 1.00
> 0.00 conf H
> ATOM 61 O1 MOL 371 -9.981 1.799 8.008 1.00
> 0.00 conf O
> ATOM 62 H7 MOL 371 -9.203 1.684 8.533 1.00
> 0.00 conf H
> ATOM 63 O2 MOL 371 -8.900 -0.615 8.667 1.00
> 0.00 conf O
> ATOM 64 H8 MOL 371 -8.521 -1.467 8.488 1.00
> 0.00 conf H
> ATOM 65 C8 MOL 371 -12.693 -2.092 7.106 1.00
> 0.00 conf C
> ATOM 66 H81 MOL 371 -12.768 -1.253 7.837 1.00
> 0.00 conf H
> ATOM 67 H82 MOL 371 -12.658 -3.092 7.598 1.00
> 0.00 conf H
> ATOM 68 H83 MOL 371 -13.633 -2.245 6.526 1.00
> 0.00 conf H
> ATOM 69 C14 MOL 371 -13.471 -3.647 4.064 1.00
> 0.00 conf C
> ATOM 70 1H14 MOL 371 -14.075 -3.084 4.813 1.00
> 0.00 conf H
> ATOM 71 2H14 MOL 371 -13.353 -4.717 4.356 1.00
> 0.00 conf H
> ATOM 72 3H14 MOL 371 -14.032 -3.789 3.111 1.00
> 0.00 conf H
> ATOM 73 C23 MOL 371 -13.126 -6.587 1.564 1.00
> 0.00 conf C
> ATOM 74 O4 MOL 371 -13.495 -7.063 2.589 1.00
> 0.00 conf O
> ATOM 75 O3 MOL 371 -13.994 -6.269 0.602 1.00
> 0.00 conf O
> ATOM 76 H25 MOL 371 -14.423 -5.458 0.857 1.00
> 0.00 conf H
> ATOM 77 C27 MOL 371 -9.279 -9.157 1.857 1.00
> 0.00 conf C
> ATOM 78 1H27 MOL 371 -10.354 -9.172 2.151 1.00
> 0.00 conf H
> ATOM 79 2H27 MOL 371 -8.594 -9.328 2.720 1.00
> 0.00 conf H
> ATOM 80 3H27 MOL 371 -8.985 -10.047 1.253 1.00
> 0.00 conf H
> TER 81 MOL 371
The prep file:

> 0 0 2
>
> This is a remark line
> molecule.res
> MOL XYZ 0
> CHANGE OMIT DU BEG
> 0.0000
> 1 DUMM DU M 999.000 999.0 -999.0 .00000
> 2 DUMM DU M 999.000 -999.0 999.0 .00000
> 3 DUMM DU M -999.000 999.0 999.0 .00000
> 4 C1 c3 M 3.330000 1.558000 -0.876000 -0.26830
> 5 H1 hc E 2.886000 2.155000 -0.086000 0.07360
> 6 H2 hc E 3.055000 2.028000 -1.816000 0.07360
> 7 C8 c3 B 2.789000 0.111000 -0.811000 0.12930
> 8 C9 c2 S 1.241000 0.119000 -0.714000 -0.08260
> 9 C10 ce B 0.523000 1.053000 -1.329000 -0.14660
> 10 H10 ha E 0.994000 1.844000 -1.882000 0.11190
> 11 C11 ce B -0.942000 1.057000 -1.320000 -0.13250
> 12 H11 ha E -1.441000 1.676000 -2.048000 0.12980
> 13 C18 c2 E -1.646000 0.354000 -0.444000 -0.27870
> 14 C27 c3 3 3.179000 -0.602000 -2.133000 -0.31580
> 15 H37 hc E 4.221000 -0.466000 -2.383000 0.07810
> 16 H38 hc E 2.594000 -0.187000 -2.945000 0.07810
> 17 H39 hc E 2.995000 -1.667000 -2.114000 0.07810
> 18 C2 c3 M 4.845000 1.644000 -0.728000 0.26120
> 19 H3 h1 E 5.349000 1.161000 -1.558000 0.02700
> 20 O2 oh S 5.267000 2.994000 -0.668000 -0.73060
> 21 H36 ho E 5.149000 3.407000 -1.512000 0.44140
> 22 C3 c3 M 5.318000 1.015000 0.569000 0.20960
> 23 H4 h1 E 4.850000 1.581000 1.375000 0.05150
> 24 O1 oh S 6.712000 1.123000 0.676000 -0.71940
> 25 H35 ho E 6.940000 2.029000 0.509000 0.45500
> 26 C4 c3 M 4.901000 -0.461000 0.729000 0.31050
> 27 C25 c3 3 5.203000 -0.844000 2.194000 -0.36920
> 28 H29 hc E 6.222000 -0.571000 2.440000 0.09170
> 29 H30 hc E 5.100000 -1.909000 2.365000 0.09170
> 30 H31 hc E 4.542000 -0.328000 2.885000 0.09170
> 31 C26 c3 3 5.751000 -1.388000 -0.159000 -0.36920
> 32 H32 hc E 5.762000 -1.103000 -1.202000 0.09170
> 33 H33 hc E 5.389000 -2.409000 -0.100000 0.09170
> 34 H34 hc E 6.777000 -1.379000 0.183000 0.09170
> 35 C5 c3 M 3.358000 -0.549000 0.486000 0.15090
> 36 H5 hc E 2.938000 0.058000 1.289000 -0.04270
> 37 C6 c3 M 2.759000 -1.947000 0.671000 -0.45840
> 38 H6 hc E 2.924000 -2.565000 -0.203000 0.12220
> 39 H7 hc E 3.235000 -2.464000 1.495000 0.12220
> 40 C7 c3 M 1.272000 -1.824000 0.993000 -0.02080
> 41 H8 hc E 1.207000 -1.353000 1.964000 0.02690
> 42 H9 hc E 0.840000 -2.813000 1.109000 0.02690
> 43 C12 c3 M 0.448000 -1.039000 -0.056000 0.27470
> 44 C28 c3 3 0.109000 -2.029000 -1.206000 -0.34530
> 45 H40 hc E 1.019000 -2.372000 -1.681000 0.08400
> 46 H41 hc E -0.509000 -1.573000 -1.965000 0.08400
> 47 H42 hc E -0.398000 -2.915000 -0.843000 0.08400
> 48 C13 c3 M -0.868000 -0.452000 0.610000 0.28130
> 49 C14 c3 3 -0.530000 0.539000 1.757000 -0.29000
> 50 H12 hc E 0.075000 1.364000 1.405000 0.05850
> 51 H13 hc E -0.008000 0.058000 2.575000 0.05850
> 52 H14 hc E -1.438000 0.955000 2.174000 0.05850
> 53 C15 c3 M -1.728000 -1.592000 1.216000 0.00530
> 54 H15 hc E -1.684000 -2.477000 0.597000 -0.00870
> 55 H16 hc E -1.309000 -1.881000 2.174000 -0.00870
> 56 C16 c3 M -3.207000 -1.244000 1.409000 -0.19060
> 57 H17 hc E -3.320000 -0.454000 2.141000 0.05540
> 58 H18 hc E -3.721000 -2.110000 1.809000 0.05540
> 59 C17 c3 M -3.867000 -0.804000 0.091000 0.24660
> 60 C29 c B -3.755000 -1.910000 -0.956000 0.63840
> 61 O3 o E -3.481000 -1.762000 -2.103000 -0.58110
> 62 O4 oh S -4.077000 -3.112000 -0.474000 -0.66650
> 63 H43 ho E -4.037000 -3.732000 -1.195000 0.47000
> 64 C19 c3 M -3.171000 0.472000 -0.434000 0.10070
> 65 H19 hc E -3.470000 0.601000 -1.466000 0.01350
> 66 C20 c3 M -3.617000 1.737000 0.338000 -0.18490
> 67 H20 hc E -3.228000 1.712000 1.349000 0.03210
> 68 H21 hc E -3.151000 2.595000 -0.137000 0.03210
> 69 C21 c3 M -5.138000 1.955000 0.422000 0.51420
> 70 C22 c3 3 -5.419000 3.141000 1.356000 -0.38690
> 71 H22 hc E -4.965000 4.053000 0.978000 0.07650
> 72 H23 hc E -5.024000 2.962000 2.352000 0.07650
> 73 H24 hc E -6.487000 3.318000 1.450000 0.07650
> 74 C30 c3 3 -5.734000 2.284000 -0.958000 -0.38690
> 75 H44 hc E -5.571000 1.502000 -1.690000 0.07650
> 76 H45 hc E -5.293000 3.195000 -1.353000 0.07650
> 77 H46 hc E -6.806000 2.444000 -0.883000 0.07650
> 78 C23 c3 M -5.770000 0.685000 1.014000 -0.09650
> 79 H25 hc E -6.854000 0.779000 1.028000 0.00540
> 80 H26 hc E -5.462000 0.592000 2.053000 0.00540
> 81 C24 c3 M -5.397000 -0.587000 0.253000 -0.10380
> 82 H27 hc E -5.822000 -1.451000 0.753000 0.02960
> 83 H28 hc E -5.850000 -0.553000 -0.734000 0.02960
>
>
> LOOP
> C5 C8
> C12 C9
> C13 C18
> C19 C18
> C24 C17
>
> IMPROPER
> C12 C8 C9 C10
> C9 C11 C10 H10
> C18 C10 C11 H11
> C13 C19 C18 C11
> C17 O3 C29 O4
>
> DONE
> STOP

The tleap.in :
> source leaprc.ff03
> source leaprc.gaff
> #source leaprc.ff99
> #loadoff /usr/local/prog/amber8/dat/leap/lib/ions94.lib
> loadamberparams cal.frcmod
> loadamberprep cal.prep
> loadamberprep mdb.prep
> lig=loadpdb mdb.pdb
> #salvamos los parámetros
> saveamberparm lig mdb.parm mdb.crd
> savepdb lig mdbtleap.pdb
> quit
>
and the error of tleap was the next:

> -I: Adding /amber9/dat/leap/prep to search path.
> -I: Adding /amber9/dat/leap/lib to search path.
> -I: Adding /amber9/dat/leap/parm to search path.
> -I: Adding /amber9/dat/leap/cmd to search path.
> -f: Source question_amber.in.
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./question_amber.in
> ----- Source: /usr/local/prog/amber9/dat/leap/cmd/leaprc.ff03
> ----- Source of /usr/local/prog/amber9/dat/leap/cmd/leaprc.ff03 done
> Log file: ./leap.log
> Loading parameters: /usr/local/prog/amber9/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters: /usr/local/prog/amber9/dat/leap/parm/frcmod.ff03
> Reading force field modification type file (frcmod)
> Reading title:
> Duan et al ff03 phi psi torsions
> Loading library: /amber9/dat/leap/lib/ions94.lib
> Loading library: /amber9/dat/leap/lib/solvents.lib
> Loading library: /amber9/dat/leap/lib/all_nucleic94.lib
> Loading library: /amber9/dat/leap/lib/all_aminoct94.lib
> Loading library: /amber9/dat/leap/lib/all_aminont94.lib
> Loading library: /amber9/dat/leap/lib/all_amino03.lib
> ----- Source: /amber9/dat/leap/cmd/leaprc.gaff
> ----- Source of /amber9/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /amber9/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic mol., add. info. at the end
> (June, 2003)
> Loading parameters: ./cal.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Ca2+ and Mn2+ vdw parameters from Concanavalin A study
> Loading Prep file: ./cal.prep
> Loading Prep file: ./mdb.prep
> Loading PDB file: ./mdb.pdb
> -- residue 371: duplicate [ H12] atoms (total 2)
>
> ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
> (same-name atoms are reduced to a single atom)
>
> Created a new atom named: H151 within residue: .R<MOL 371>
> Created a new atom named: H152 within residue: .R<MOL 371>
> Created a new atom named: H131 within residue: .R<MOL 371>
> Created a new atom named: H132 within residue: .R<MOL 371>
> Created a new atom named: H191 within residue: .R<MOL 371>
> Created a new atom named: H192 within residue: .R<MOL 371>
> Created a new atom named: H193 within residue: .R<MOL 371>
> Created a new atom named: H251 within residue: .R<MOL 371>
> Created a new atom named: H252 within residue: .R<MOL 371>
> Created a new atom named: H241 within residue: .R<MOL 371>
> Created a new atom named: H242 within residue: .R<MOL 371>
> Created a new atom named: H211 within residue: .R<MOL 371>
> Created a new atom named: H212 within residue: .R<MOL 371>
> Created a new atom named: H281 within residue: .R<MOL 371>
> Created a new atom named: H282 within residue: .R<MOL 371>
> Created a new atom named: H283 within residue: .R<MOL 371>
> Created a new atom named: H291 within residue: .R<MOL 371>
> Created a new atom named: H292 within residue: .R<MOL 371>
> Created a new atom named: H301 within residue: .R<MOL 371>
> Created a new atom named: H302 within residue: .R<MOL 371>
> Created a new atom named: H91 within residue: .R<MOL 371>
> Created a new atom named: H92 within residue: .R<MOL 371>
> Created a new atom named: H93 within residue: .R<MOL 371>
> Created a new atom named: H71 within residue: .R<MOL 371>
> Created a new atom named: H72 within residue: .R<MOL 371>
> Created a new atom named: H73 within residue: .R<MOL 371>
> Created a new atom named: H81 within residue: .R<MOL 371>
> Created a new atom named: H82 within residue: .R<MOL 371>
> Created a new atom named: H83 within residue: .R<MOL 371>
> Created a new atom named: H141 within residue: .R<MOL 371>
> Created a new atom named: H142 within residue: .R<MOL 371>
> Created a new atom named: H143 within residue: .R<MOL 371>
> Created a new atom named: H271 within residue: .R<MOL 371>
> Created a new atom named: H272 within residue: .R<MOL 371>
> Created a new atom named: H273 within residue: .R<MOL 371>
> total atoms in file: 80
> Leap added 36 missing atoms according to residue templates:
> 36 H / lone pairs
> The file contained 35 atoms not in residue templates
> Checking Unit.
> WARNING: There is a bond of 3.872151 angstroms between:
> ------- .R<MOL 371>.A<C21 66> and .R<MOL 371>.A<C23 75>
> WARNING: There is a bond of 3.431391 angstroms between:
> ------- .R<MOL 371>.A<C19 61> and .R<MOL 371>.A<C20 63>
> WARNING: There is a bond of 4.421972 angstroms between:
> ------- .R<MOL 371>.A<C29 57> and .R<MOL 371>.A<O3 58>
> WARNING: There is a bond of 4.573110 angstroms between:
> ------- .R<MOL 371>.A<C29 57> and .R<MOL 371>.A<O4 59>
> WARNING: There is a bond of 5.049533 angstroms between:
> ------- .R<MOL 371>.A<C17 56> and .R<MOL 371>.A<C29 57>
> WARNING: There is a bond of 6.204343 angstroms between:
> ------- .R<MOL 371>.A<C15 50> and .R<MOL 371>.A<H16 52>
> WARNING: There is a bond of 5.165353 angstroms between:
> ------- .R<MOL 371>.A<C15 50> and .R<MOL 371>.A<C16 53>
> WARNING: There is a bond of 4.057679 angstroms between:
> ------- .R<MOL 371>.A<C14 46> and .R<MOL 371>.A<H12 47>
> WARNING: There is a bond of 6.845533 angstroms between:
> ------- .R<MOL 371>.A<C12 40> and .R<MOL 371>.A<C28 41>
> WARNING: There is a bond of 3.772516 angstroms between:
> ------- .R<MOL 371>.A<C12 40> and .R<MOL 371>.A<C13 45>
> WARNING: There is a bond of 5.132189 angstroms between:
> ------- .R<MOL 371>.A<C7 37> and .R<MOL 371>.A<H8 38>
> WARNING: There is a bond of 5.881813 angstroms between:
> ------- .R<MOL 371>.A<C7 37> and .R<MOL 371>.A<C12 40>
> WARNING: There is a bond of 4.781341 angstroms between:
> ------- .R<MOL 371>.A<C6 34> and .R<MOL 371>.A<H7 36>
> WARNING: There is a bond of 3.377123 angstroms between:
> ------- .R<MOL 371>.A<C6 34> and .R<MOL 371>.A<C7 37>
> WARNING: There is a bond of 6.744391 angstroms between:
> ------- .R<MOL 371>.A<C4 23> and .R<MOL 371>.A<C25 24>
> WARNING: There is a bond of 10.329722 angstroms between:
> ------- .R<MOL 371>.A<C4 23> and .R<MOL 371>.A<C26 28>
> WARNING: There is a bond of 4.189099 angstroms between:
> ------- .R<MOL 371>.A<C2 15> and .R<MOL 371>.A<O2 17>
> WARNING: There is a bond of 3.915034 angstroms between:
> ------- .R<MOL 371>.A<C18 10> and .R<MOL 371>.A<C13 45>
> WARNING: There is a bond of 4.020921 angstroms between:
> ------- .R<MOL 371>.A<C11 8> and .R<MOL 371>.A<H11 9>
> WARNING: There is a bond of 5.003318 angstroms between:
> ------- .R<MOL 371>.A<C9 5> and .R<MOL 371>.A<C10 6>
> WARNING: There is a bond of 6.152030 angstroms between:
> ------- .R<MOL 371>.A<C9 5> and .R<MOL 371>.A<C12 40>
> WARNING: There is a bond of 4.779332 angstroms between:
> ------- .R<MOL 371>.A<C8 4> and .R<MOL 371>.A<C9 5>
> WARNING: There is a bond of 9.440425 angstroms between:
> ------- .R<MOL 371>.A<C8 4> and .R<MOL 371>.A<C27 11>
> WARNING: There is a bond of 3.133565 angstroms between:
> ------- .R<MOL 371>.A<C8 4> and .R<MOL 371>.A<C5 32>
> FATAL: Atom .R<MOL 371>.A<H151 81> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H152 82> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H131 83> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H132 84> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H191 85> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H192 86> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H193 87> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H251 88> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H252 89> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H241 90> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H242 91> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H211 92> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H212 93> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H281 94> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H282 95> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H283 96> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H291 97> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H292 98> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H301 99> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H302 100> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H91 101> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H92 102> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H93 103> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H71 104> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H72 105> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H73 106> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H81 107> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H82 108> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H83 109> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H141 110> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H142 111> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H143 112> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H271 113> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H272 114> does not have a type.
> FATAL: Atom .R<MOL 371>.A<H273 115> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Writing pdb file: mdbtleap.pdb
> Quit
>

Thanks in advance for your help.

Henar

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