Hi Sourav,
you didnt tell us what steps you performed before seeing this error, so I
can only offer a guess. To use a non-standard residue in Amber it needs a
residue description and force field parameters defined, as described in
this tutorial: http://ambermd.org/tutorials/basic/tutorial4b/
Doing the same steps for a Se-containing compound would not be different in
principle, though you may run into issues in e.g. QM charge fitting if the
element is not supported in your QM program of choice.
If you have done all these steps already, then the error you see is likely
due to atom/residue name mismatches between your input pdb and parameter
files.
Kind Regards,
Thomas
On Wed, Sep 20, 2023 at 7:29 AM Sourav Bhowmik via AMBER <amber.ambermd.org>
wrote:
> **Warning** The sender address (Sourav Bhowmik via AMBER ) can not be
> verified, sender email address could be spoofed. Please take care to
> proceed.
> Respected Sir/Madam,
> I tried to generate topology files using ambertools programme tleap for a
> system which contains an unusual atom selenium. This programme ended up
> with a fatal error. Could you please guide me how to generate the files for
> the systems which contain unusual atoms like selenium. Please find the
> below text for your reference.
>
> /home/apps/amber20/amber20/bin/teLeap: Warning!
> The unperturbed charge of the unit (-0.060000) is not zero.
> FATAL: Atom .R<UNK 61>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 62>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 63>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 64>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 65>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 66>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 67>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 68>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 69>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 70>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 71>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 72>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 73>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 74>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 75>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 76>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 77>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 78>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 79>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 80>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 81>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 82>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 83>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 84>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 85>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 86>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 87>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 88>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 89>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 90>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 91>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 92>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 93>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 94>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 95>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 96>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 97>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 98>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 99>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 100>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 101>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 102>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 103>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 104>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 105>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 106>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 107>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 108>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 109>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 110>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 111>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 112>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 113>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 114>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 115>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 116>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 117>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 118>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 119>.A<Se1 62> does not have a type.
> FATAL: Atom .R<UNK 120>.A<Se1 62> does not have a type.
>
> /home/apps/amber20/amber20/bin/teLeap: Fatal Error!
> Failed to generate parameters
>
> Exiting LEaP: Errors = 1; Warnings = 3; Notes = 0.
>
> Regards
> Sourav Bhowmik
> Research Scholar
> IIT Indore
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>
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Wed Sep 20 2023 - 00:00:02 PDT
