Urszula,
- I would avoid doing twice the same command in LEaP (for instance LYA
= loadmol2 LYA.mol2)...
- the total charge of your peptide is: 1.999800
-> We released yesterday automatic rounding off error corrections
for multiple molecule in R.E.D. Server and R.E.D. Server development
(Simply check that a correct number of counterions is added if you
use explicit solvent conditions)
- CT - OS - CG angle parameter misses; CT-OS-CT can be used for
CT-OS-CG and added in a frcmod file...
regards, 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 Wed May 16 2012 - 06:30:02 PDT
