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From: Tsibela German Tebello Mofokeng <1754789.students.wits.ac.za>

Date: Wed, 7 Dec 2016 15:23:24 +0200

Dear Amber users

I would like to perform a constant pH MD calculation (explicit solvent) of

a peptide containing hydroxyproline residues using Amber14. I get an error

message when trying to create the topology and coordinate files by using

the following commands:

source leaprc.constph

*>Unitx = loadPDB peptideX.pdb
*

*>check Unitx
*

FATAL: Atom .R<HYP 3>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 3>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 3>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 6>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 6>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 6>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 9>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 9>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 9>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 15>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 15>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 15>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 18>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 18>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 18>.A<HG 18> does not have a type.

I then checked the Amber14 reference manual p395, it seem like running the

following command(source leaprc.constph)loads force field (ff12SB).

Which command can I use in Amber14 to load force field (ff14SB) instead of

(ff12SB)?

I know force field (ff14SB) has parameters for Hydroxyproline.

Regards

Tebello

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Received on Wed Dec 07 2016 - 05:30:02 PST

Date: Wed, 7 Dec 2016 15:23:24 +0200

Dear Amber users

I would like to perform a constant pH MD calculation (explicit solvent) of

a peptide containing hydroxyproline residues using Amber14. I get an error

message when trying to create the topology and coordinate files by using

the following commands:

source leaprc.constph

FATAL: Atom .R<HYP 3>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 3>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 3>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 6>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 6>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 6>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 9>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 9>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 9>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 15>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 15>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 15>.A<HG 18> does not have a type.

FATAL: Atom .R<HYP 18>.A<HD22 16> does not have a type.

FATAL: Atom .R<HYP 18>.A<HD23 17> does not have a type.

FATAL: Atom .R<HYP 18>.A<HG 18> does not have a type.

I then checked the Amber14 reference manual p395, it seem like running the

following command(source leaprc.constph)loads force field (ff12SB).

Which command can I use in Amber14 to load force field (ff14SB) instead of

(ff12SB)?

I know force field (ff14SB) has parameters for Hydroxyproline.

Regards

Tebello

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Wed Dec 07 2016 - 05:30:02 PST

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