- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Jerrano Bowleg <jlb1692.msstate.edu>

Date: Thu, 18 May 2017 14:48:22 -0500

I am attempting to use amber to analyse a cMYC G quadruplex structure. When

I load the pdb onto xLEaP and attempt to create prmtop and inpcrd files

using the command

saveamberparm cMYC121_vac.prmtop cMYC_vac.inpcrd

I get the following error

Checking Unit.

FATAL: Atom .R<DT5 1>.A<P 31> does not have a type.

FATAL: Atom .R<DT5 1>.A<OP1 32> does not have a type.

FATAL: Atom .R<DT5 1>.A<OP2 33> does not have a type.

FATAL: Atom .R<DT5 1>.A<OP3 34> does not have a type.

FATAL: Atom .R<DT5 1>.A<H11 35> does not have a type.

FATAL: Atom .R<DT 10>.A<N9 33> does not have a type.

FATAL: Atom .R<DT 10>.A<N7 34> does not have a type.

FATAL: Atom .R<DT 10>.A<C8 35> does not have a type.

FATAL: Atom .R<DT 10>.A<H8 36> does not have a type.

FATAL: Atom .R<DT 10>.A<H2 37> does not have a type.

FATAL: Atom .R<DT 10>.A<N6 38> does not have a type.

FATAL: Atom .R<DT 10>.A<H61 39> does not have a type.

FATAL: Atom .R<DT 10>.A<H62 40> does not have a type.

FATAL: Atom .R<DA3 23>.A<'HO3 34> does not have a type.

Failed to generate parameters

Parameter file was not saved.

Is there a command to tell Amber that it is dealing with this, or any way

around this problem?

Many thanks,

Date: Thu, 18 May 2017 14:48:22 -0500

I am attempting to use amber to analyse a cMYC G quadruplex structure. When

I load the pdb onto xLEaP and attempt to create prmtop and inpcrd files

using the command

saveamberparm cMYC121_vac.prmtop cMYC_vac.inpcrd

I get the following error

Checking Unit.

FATAL: Atom .R<DT5 1>.A<P 31> does not have a type.

FATAL: Atom .R<DT5 1>.A<OP1 32> does not have a type.

FATAL: Atom .R<DT5 1>.A<OP2 33> does not have a type.

FATAL: Atom .R<DT5 1>.A<OP3 34> does not have a type.

FATAL: Atom .R<DT5 1>.A<H11 35> does not have a type.

FATAL: Atom .R<DT 10>.A<N9 33> does not have a type.

FATAL: Atom .R<DT 10>.A<N7 34> does not have a type.

FATAL: Atom .R<DT 10>.A<C8 35> does not have a type.

FATAL: Atom .R<DT 10>.A<H8 36> does not have a type.

FATAL: Atom .R<DT 10>.A<H2 37> does not have a type.

FATAL: Atom .R<DT 10>.A<N6 38> does not have a type.

FATAL: Atom .R<DT 10>.A<H61 39> does not have a type.

FATAL: Atom .R<DT 10>.A<H62 40> does not have a type.

FATAL: Atom .R<DA3 23>.A<'HO3 34> does not have a type.

Failed to generate parameters

Parameter file was not saved.

Is there a command to tell Amber that it is dealing with this, or any way

around this problem?

Many thanks,

-- Jerrano L. Bowleg PhD Student Department of Chemistry Gwaltney Lab- Hand Lab 1126 Mississippi State University _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu May 18 2017 - 13:00:03 PDT

Custom Search