Dear Amber users,
I used tleap to parametrize a complex og a kinase bound to ATP and 2 MG2+ ions.
I used the following input file:
source leaprc.ff99SB
loadamberparams ATPphos.frcmod
loadamberprep ATP.prep
COMPLEX = loadpdb PknGATP_init_min_vac.pdb
alignAxes COMPLEX
addions COMPLEX Na+ 6
solvatebox COMPLEX TIP3PBOX 8.0
saveamberparm COMPLEX PknGATP_wt.prmtop PknGATP_wt.inpcrd
quit
The log file contained the following messages:
Loading parameters: ./ATPphos.frcmod
Loading Prep file: ./ATP.prep
Loading PDB file: ./PknGATP_init_min_vac.pdb
One sided connection. Residue: MG2 missing connect0 atom.
etc...
What does the last sentence mean?
Was the Mg2+ well parametrized or not ?
Thank you.
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: George Patargias [gpat.bioacademy.gr]
Sent: Thursday, July 17, 2014 8:21 AM
To: AMBER Mailing List
Subject: Re: [AMBER] ATP parameters: tleap error
Hello Valentina,
The residue name in your ATP.pdb should be "atp" (small-case). Also make
sure the atom names in the ATP.pdb match the atom names in ATP.prep and
ATPphos.frcmod.
George
> Dear Amber users
>
> I I want to run a MD of a kinase in complex with ATP.
> To build ATP parameters I used files .frcmod and .prep found on
> http://www.pharmacy.manchester.ac.uk/bryce/amber/ and I loaded them in
> tleap.
>
> I used the following script:
>
> source leaprc.ff99SB
> loadamberparams ATPphos.frcmod
> loadamberprpe ATP.prep
> ATP = loadpdb ATP.pdb
> saveoff ATP ATP.lib
> saveamberparm ATP ATP.prmtop ATP.inpcrd
> quit
>
> I got the following error:
>
> Loading parameters: ./ATPphos.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> # Modifications to the AMBER94 force field for polyphosphates
> ERROR: syntax error
>
> Loading PDB file: ./ATP.pdb
> Unknown residue: ATP number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: ATP sequence: 1279
> Created a new atom named: PG within residue: .R<ATP 1279>
> Created a new atom named: O1G within residue: .R<ATP 1279>
> Created a new atom named: O2G within residue: .R<ATP 1279>
> Created a new atom named: O3 within residue: .R<ATP 1279>
> Created a new atom named: PB within residue: .R<ATP 1279>
> Created a new atom named: O1B within residue: .R<ATP 1279>
> Created a new atom named: O2B within residue: .R<ATP 1279>
> Created a new atom named: O1 within residue: .R<ATP 1279>
> Created a new atom named: PA within residue: .R<ATP 1279>
> Created a new atom named: O1A within residue: .R<ATP 1279>
> Created a new atom named: O2A within residue: .R<ATP 1279>
> Created a new atom named: O3A within residue: .R<ATP 1279>
> Created a new atom named: O5' within residue: .R<ATP 1279>
> Created a new atom named: C5' within residue: .R<ATP 1279>
> Created a new atom named: C4' within residue: .R<ATP 1279>
> Created a new atom named: O4' within residue: .R<ATP 1279>
> Created a new atom named: C3' within residue: .R<ATP 1279>
> Created a new atom named: O3' within residue: .R<ATP 1279>
> Created a new atom named: C2' within residue: .R<ATP 1279>
> Created a new atom named: O2' within residue: .R<ATP 1279>
> Created a new atom named: C1' within residue: .R<ATP 1279>
> Created a new atom named: N9 within residue: .R<ATP 1279>
> Created a new atom named: C8 within residue: .R<ATP 1279>
> Created a new atom named: N7 within residue: .R<ATP 1279>
> Created a new atom named: C5 within residue: .R<ATP 1279>
> Created a new atom named: C6 within residue: .R<ATP 1279>
> Created a new atom named: N6 within residue: .R<ATP 1279>
> Created a new atom named: N1 within residue: .R<ATP 1279>
> Created a new atom named: C2 within residue: .R<ATP 1279>
> Created a new atom named: N3 within residue: .R<ATP 1279>
> Created a new atom named: C4 within residue: .R<ATP 1279>
> Created a new atom named: H5'1 within residue: .R<ATP 1279>
> Created a new atom named: H5'2 within residue: .R<ATP 1279>
> Created a new atom named: H4' within residue: .R<ATP 1279>
> Created a new atom named: H3' within residue: .R<ATP 1279>
> Created a new atom named: HO3' within residue: .R<ATP 1279>
> Created a new atom named: H2' within residue: .R<ATP 1279>
> Created a new atom named: HO2' within residue: .R<ATP 1279>
> Created a new atom named: H1' within residue: .R<ATP 1279>
> Created a new atom named: H8 within residue: .R<ATP 1279>
> Created a new atom named: H61 within residue: .R<ATP 1279>
> Created a new atom named: H62 within residue: .R<ATP 1279>
> Created a new atom named: H2 within residue: .R<ATP 1279>
> total atoms in file: 43
> The file contained 43 atoms not in residue templates
> Building topology.
> Building atom parameters.
> Checking Unit.
> FATAL: Atom .R<ATP 1279>.A<PG 1> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O1G 2> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O2G 3> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O3 4> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<PB 5> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O1B 6> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O2B 7> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O1 8> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<PA 9> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O1A 10> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O2A 11> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O3A 12> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O5' 13> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C5' 14> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C4' 15> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O4' 16> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C3' 17> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O3' 18> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C2' 19> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<O2' 20> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C1' 21> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<N9 22> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C8 23> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<N7 24> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C5 25> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C6 26> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<N6 27> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<N1 28> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C2 29> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<N3 30> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<C4 31> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H5'1 32> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H5'2 33> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H4' 34> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H3' 35> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<HO3' 36> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H2' 37> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<HO2' 38> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H1' 39> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H8 40> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H61 41> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H62 42> does not have a type.
> FATAL: Atom .R<ATP 1279>.A<H2 43> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Quit
>
> It looked like tleap did not recognize the ATP atom types.
> I changed all atom names in the pdb file of ATP according to the atom
> types used in the file .prep and I got the same error.
>
> Any suggestion to understand and solve that problem?
>
> Thank you
> Valentina
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
> Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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Received on Wed Aug 13 2014 - 08:00:10 PDT
