AMBER Archive (2009)

Subject: RE: [AMBER] Amber - Leap- SolvateBox help

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 20 2009 - 00:20:50 CDT

Hi Shubhra

 

I am copying this message to the amber mailing list which is where such
questions should be posted. See http://ambermd.org/ for signup details.

 

You need to identify what the name of your residue should be here. At the
moment it is just named C which is not a valid carbohydrate residue in the
GLYCAM force field. I suggest starting by reading the paper describing the
GLYCAM 06 force field. It is cited in the AMBER manual I believe. This
explains the naming convention for carbohydrates. Once you have this you can
edit your pdb to have the correct residue name. You then need to adjust the
atom names to also have the correct names. Edit XXX where XXX is the
corresponding residue name you identify will allow you to look at the atom
names and compare them with your structure so you can assign the correct
names.

 

Leap should then be able to identify your residue and add the correct bonds
and assign the correct parameters etc...

 

Good luck,

Ross

 

From: shubhgiiar_at_gmail.com [mailto:shubhgiiar_at_gmail.com] On Behalf Of
Shubhra Gupta
Sent: Sunday, May 17, 2009 9:51 PM
To: ross_at_rosswalker.co.uk
Subject: Re: [AMBER] Amber - Leap- SolvateBox help

 

Dear Prof. Walker:

Attached one is the file of carbohydrate in pdb format, which I am using for
analysis.
But whenever I used to execute "saveamberparm", it is givening below error.
I do not know how to convert the file in proper format.

FATAL: Atom .R<C 4>.A<C1 1> does not have a type.
FATAL: Atom .R<C 4>.A<C2 2> does not have a type.
FATAL: Atom .R<C 4>.A<C3 3> does not have a type.
FATAL: Atom .R<C 4>.A<C4 4> does not have a type.
FATAL: Atom .R<C 4>.A<C5 5> does not have a type.
FATAL: Atom .R<C 4>.A<C6 6> does not have a type.
FATAL: Atom .R<C 4>.A<O2 7> does not have a type.
FATAL: Atom .R<C 4>.A<O3 8> does not have a type.
FATAL: Atom .R<C 4>.A<O4 9> does not have a type.
FATAL: Atom .R<C 4>.A<O5 10> does not have a type.
FATAL: Atom .R<C 4>.A<O6 11> does not have a type.
FATAL: Atom .R<C 5>.A<O6 1> does not have a type.
FATAL: Atom .R<C 5>.A<C6 2> does not have a type.
FATAL: Atom .R<C 5>.A<C5 3> does not have a type.
FATAL: Atom .R<C 5>.A<O5 4> does not have a type.
FATAL: Atom .R<C 5>.A<C1 5> does not have a type.
FATAL: Atom .R<C 5>.A<O1 6> does not have a type.
FATAL: Atom .R<C 5>.A<CM 7> does not have a type.
FATAL: Atom .R<C 5>.A<C2 8> does not have a type.
FATAL: Atom .R<C 5>.A<N2 9> does not have a type.
FATAL: Atom .R<C 5>.A<C7 10> does not have a type.
FATAL: Atom .R<C 5>.A<O7 11> does not have a type.
FATAL: Atom .R<C 5>.A<C8 12> does not have a type.
FATAL: Atom .R<C 5>.A<C3 13> does not have a type.
FATAL: Atom .R<C 5>.A<O3 14> does not have a type.
FATAL: Atom .R<C 5>.A<C4 15> does not have a type.
FATAL: Atom .R<C 5>.A<O4 16> does not have a type.
Failed to generate parameters
Parameter file was not saved.

I will appreciate your help.

Thank You,
Shubhra Gupta

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