AMBER Archive (2009)

Subject: Re: [AMBER] Parameter file not saved

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon May 04 2009 - 07:19:14 CDT

the key is in the message right at the start: "Unknown residue: BGF".
Amber does not know how to handle this. you will need to learn how to build
a new residue type. It can be done, but I suggest only doing it after you
are comfortable with MD simulations and have done some background reading on
force fields so that you understand the various parameters. Then, work
through the tutorials, eventually getting to the ones that show you how to
build a new residue. make sure to read at least a few papers from the
literature that show successful work of the type you want to do- reading the
manual is not enough, read the peer-reviewed literature too.

On Mon, May 4, 2009 at 8:03 AM, Remya S R
<amm07bi022_at_students.amrita.ac.in>wrote:

> Dear Amber users,
> I got the following error when tried to run "tleap"
> during the simulation of DNA complexed with 2,5' bis(4-guanyl)furan. Please
> help me solve this!!!!!
>
> The error is as follows
> Loading PDB file: /home/student/remya/227D/complex_setup/227d_dna_BGF.pdb
> Unknown residue: BGF number: 24 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: BGF sequence: 25
> Created a new atom named: CA within residue: .R<BGF 25>
> Created a new atom named: CB within residue: .R<BGF 25>
> Created a new atom named: CB' within residue: .R<BGF 25>
> Created a new atom named: CA' within residue: .R<BGF 25>
> Created a new atom named: O1 within residue: .R<BGF 25>
> Created a new atom named: C1 within residue: .R<BGF 25>
> Created a new atom named: C2 within residue: .R<BGF 25>
> Created a new atom named: C3 within residue: .R<BGF 25>
> Created a new atom named: C4 within residue: .R<BGF 25>
> Created a new atom named: C5 within residue: .R<BGF 25>
> Created a new atom named: C6 within residue: .R<BGF 25>
> Created a new atom named: C7 within residue: .R<BGF 25>
> Created a new atom named: N1 within residue: .R<BGF 25>
> Created a new atom named: N2 within residue: .R<BGF 25>
> Created a new atom named: C1' within residue: .R<BGF 25>
> Created a new atom named: C2' within residue: .R<BGF 25>
> Created a new atom named: C3' within residue: .R<BGF 25>
> Created a new atom named: C4' within residue: .R<BGF 25>
> Created a new atom named: C5' within residue: .R<BGF 25>
> Created a new atom named: C6' within residue: .R<BGF 25>
> Created a new atom named: C7' within residue: .R<BGF 25>
> Created a new atom named: N1' within residue: .R<BGF 25>
> Created a new atom named: N2' within residue: .R<BGF 25>
> Created a new atom named: HB within residue: .R<BGF 25>
> Created a new atom named: HB' within residue: .R<BGF 25>
> Created a new atom named: H2 within residue: .R<BGF 25>
> Created a new atom named: H3 within residue: .R<BGF 25>
> Created a new atom named: H5 within residue: .R<BGF 25>
> Created a new atom named: H6 within residue: .R<BGF 25>
> Created a new atom named: HN11 within residue: .R<BGF 25>
> Created a new atom named: HN12 within residue: .R<BGF 25>
> Created a new atom named: HN21 within residue: .R<BGF 25>
> Created a new atom named: HN22 within residue: .R<BGF 25>
> Created a new atom named: H2' within residue: .R<BGF 25>
> Created a new atom named: H3' within residue: .R<BGF 25>
> Created a new atom named: H5' within residue: .R<BGF 25>
> Created a new atom named: H6' within residue: .R<BGF 25>
> Created a new atom named: H1'1 within residue: .R<BGF 25>
> Created a new atom named: H1'2 within residue: .R<BGF 25>
> Created a new atom named: H2'1 within residue: .R<BGF 25>
> Created a new atom named: H2'2 within residue: .R<BGF 25>
> total atoms in file: 801
> The file contained 41 atoms not in residue templates
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -24.000000 is not zero.
> FATAL: Atom .R<BGF 25>.A<CA 1> does not have a type.
> FATAL: Atom .R<BGF 25>.A<CB 2> does not have a type.
> FATAL: Atom .R<BGF 25>.A<CB' 3> does not have a type.
> FATAL: Atom .R<BGF 25>.A<CA' 4> does not have a type.
> FATAL: Atom .R<BGF 25>.A<O1 5> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C1 6> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C2 7> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C3 8> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C4 9> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C5 10> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C6 11> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C7 12> does not have a type.
> FATAL: Atom .R<BGF 25>.A<N1 13> does not have a type.
> FATAL: Atom .R<BGF 25>.A<N2 14> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C1' 15> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C2' 16> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C3' 17> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C4' 18> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C5' 19> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C6' 20> does not have a type.
> FATAL: Atom .R<BGF 25>.A<C7' 21> does not have a type.
> FATAL: Atom .R<BGF 25>.A<N1' 22> does not have a type.
> FATAL: Atom .R<BGF 25>.A<N2' 23> does not have a type.
> FATAL: Atom .R<BGF 25>.A<HB 24> does not have a type.
> FATAL: Atom .R<BGF 25>.A<HB' 25> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H2 26> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H3 27> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H5 28> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H6 29> does not have a type.
> FATAL: Atom .R<BGF 25>.A<HN11 30> does not have a type.
> FATAL: Atom .R<BGF 25>.A<HN12 31> does not have a type.
> FATAL: Atom .R<BGF 25>.A<HN21 32> does not have a type.
> FATAL: Atom .R<BGF 25>.A<HN22 33> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H2' 34> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H3' 35> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H5' 36> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H6' 37> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H1'1 38> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H1'2 39> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H2'1 40> does not have a type.
> FATAL: Atom .R<BGF 25>.A<H2'2 41> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Quit
>
>
> The input file for tleap is as follows
>
> source leaprc.ff03
> source leaprc.gaff
> mods=loadamberparams /home/student/remya/227D/complex_setup/BGF.frcmod
> BGF=loadmol2 /home/student/remya/227D/complex_setup/BGF.mol2
>
> complex=loadpdb /home/student/remya/227D/complex_setup/227d_dna_BGF.pdb
>
> saveamberparm complex
> /home/student/remya/227D/complex_setup/227d_complex.prmtop
> /home/student/remya/227D/complex_setup/227d_complex.inpcrd
>
> quit
>
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