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 - 12:28:13 CST

Thank you very much for your help.
Now I can obtain the parameters file.

Henar

Junmei Wang escribió:
> Evidently, some atom names in your pdb and prepi files do not match.
> For example, there are a couple hydrogen atoms have 4-letter names
> (such as H271, H272 and H273) in pdb, while none hydrogen has 4-letter
> name in the prepi file. I used your pdb file and ran antechamber to
> generate a prep input file (antechamber -fi pdb -fo prepi -i input.pdb
> -o input.prepi -c bcc). The prep input file looks good.
>
> By the way, if you use resp charges and generate prepi directly from a
> gaussian output, you need to provide atom names information to
> antechamber. This is because gaussian output does not contain atom
> names information at all. Here is the command you may try:
>
> antechamber -fi gout -fo prepi -fa pdb -i mol.gout -o mol.prepi -a
> mol.pdb -c resp -ao name
>
> suppose your pdb file is mol.pdb and gaussian output file is mol.gout.
> "-ao name" flag tells the program only replace the atom names
> information in gout with those in mol.pdb.
>
> Best
>
> Junmei
>
> On Wed, Feb 27, 2008 at 5:14 AM, Henar Martínez <henar_at_eis.uva.es
> <mailto:henar_at_eis.uva.es>> wrote:
>
> 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
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>>
>>
> I think the pdb file was in strange form, I send you again.
>
> 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
>
> Sorry. I hope this time was good.
>
> Henar
>
>
>
>
>
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>

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