Dear Francois,
I corrected the pep1_H.pdb file and created LYA.frcmod, below are the steps that I done in xleap, there are still missing parameters for CT - OS - CG in MGR.mol2 file, any suggestions how to change them?
> glycam = loadamberparams glycam04.dat
Loading parameters: /lap/amber/11.0.17_AT1.5/dat/leap/parm/glycam04.dat
Reading title:
GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
(UNKNOWN ATOM TYPE: CG)
> MGR = loadmol2 MGR.mol2
Loading Mol2 file: ./MGR.mol2
Reading MOLECULE named MGR
> set MGR name "MGR"
> set MGR head MGR.1.N
> set MGR tail MGR.1.C
> set MGR.1 connect0 MGR.1.N
> set MGR.1 connect1 MGR.1.C
> LYA = loadamberparams LYA.params
Loading parameters: ./LYA.params
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> LYA = loadmol2 LYA.mol2
Loading Mol2 file: ./LYA.mol2
Reading MOLECULE named LYA
> LYA = loadmol2 LYA.mol2
Loading Mol2 file: ./LYA.mol2
Reading MOLECULE named LYA
> set LYA name "LYA"
> set LYA head LYA.1.N
> set LYA tail LYA.1.C
> set LYA.1 connect0 LYA.1.N
> set LYA.1 connect1 LYA.1.C
> x = loadpdb pep1_H.pdb
Loading PDB file: ./pep1_H.pdb
> check x
Checking 'x'....
WARNING: The unperturbed charge of the unit: 1.999800 is not zero.
Warning: Close contact of 1.321006 angstroms between .R<MGR 6>.A<HO6 32> and .R<GLU 8>.A<OE1 12>
Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: CT - OS - CG
There are missing parameters.
check: Warnings: 2
Unit is OK.
thank you in advance for any suggestions
/Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Dienstag, 15. Mai 2012 15:42
An: AMBER Mailing List
Betreff: Re: [AMBER] problems with added hydrogens to non standard residue
Urszula,
> I attached wrong LYA.mol2 file, but I have still errors about parameters...
For LYA.mol2:
you need to define a new atom type for the aldehydic hydrogen
create a frcmod file with this aldehyde hydrogen. I wonder if K.
Kirschner has a FF, that handles aldehyde hydrogens...
For the PDB file:
- rename the LYS residue name into LYA
- rename the LS atom names in agreement with these in LYA.mol2
regards, Francois
> _______
> Von: case [case.biomaps.rutgers.edu]
> Gesendet: Dienstag, 15. Mai 2012 15:07
> An: AMBER Mailing List
> Betreff: Re: [AMBER] problems with added hydrogens to non standard residue
>
> On Tue, May 15, 2012, Urszula Uciechowska wrote:
>>
>> I developed a lib for a terminal Lysine residue, LYA.mol2. However after
>> loading everything together with the peptide.pdb I have still errors
>> regarding the parameters,
>> I attached the files:
>>
>> LYA.mol2 - terminal Lysine
>
> This file has atom types that are just "H", "N", "C", etc. These don't
> correspond to any atom types that Amber or gaff know about.
>
>> leap.log
>
> The error in this file is in lines like this:
>
> Unit Editor: Could not find bond parameter for: C - H
>
> Basically, Amber doesn't have parameters for the atom types you have in the
> LYA.mol2 file. You probably need to generate this residue in a way that uses
> atom types Amber understands.
>
> ....dac
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Received on Tue May 15 2012 - 08:00:04 PDT
