there are really 2 questions here:
1) how do you generate library files for non-standard groups
2) how can you include selenium
for (1), look at the Amber tutorials at www.ambermd.org
for (2), you might be able to adapt the parameters for selenium included in
parm/frcmod.ff14SBmodAA
On Wed, Sep 20, 2023 at 1:29 AM Sourav Bhowmik via AMBER <amber.ambermd.org>
wrote:
> 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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Received on Wed Sep 20 2023 - 08:30:02 PDT
