AMBER Archive (2009)Subject: Re: [AMBER] Amber  Leap SolvateBox help
From: Remya S R (amm07bi022_at_students.amrita.ac.in)
Date: Tue May 19 2009  01:22:12 CDT
hai,
you can either edit the pdb file manually for the atom type or use "addPdbAtomMap"
 Original Message 
From: "Shubhra Gupta" <shubhg_at_iiar.res.in>
To: amber_at_ambermd.org
Sent: Tuesday, May 19, 2009 9:24:23 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [AMBER] Amber  Leap SolvateBox help
Dear Amber Members:
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 giving
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.
> Thank You,
> Shubhra
>
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