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From: Sourav Bhowmik via AMBER <amber.ambermd.org>

Date: Wed, 20 Sep 2023 10:58:31 +0530

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Sep 19 2023 - 22:30:02 PDT

Date: Wed, 20 Sep 2023 10:58:31 +0530

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Sep 19 2023 - 22:30:02 PDT

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