Sorry... missed a bit.
You need to change the CT atom types to CG in the prep file. I'm sure
there's some way to instruct antechamber to do that for you, but
changing the file is easy.
It might not hurt, but it will probably be safer to change your
residue name to something not already used in GLYCAM. So, make it FUC
or ALF or whatever rather than ROH.
I just tested with the following input (with the residue renamed ALF),
and it worked:
# if sleap for use in amber11: set default write14scale on
source leaprc.GLYCAM_06
loadamberprep ALF.prep
saveamberparm ALF ALF.top ALF.rst
quit
If you load a pdb, just make sure the residue names match the new prep file.
On Wed, Feb 9, 2011 at 12:18 PM, mish <smncbr.gmail.com> wrote:
> Thanks a lot. I fallowed the same procedure for alpha-L-fucose (ROH and
> 0fA). made a prepi file by antechamber and then loaded it in tleap. Then I
> changed the residue name of one pdb file of alpha-L-fucose to ROH and loaded
> this one too. Now if I check the unit it says that their are missing angle
> parametres.
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>> a=loadpdb alfuc.pdb
> Loading PDB file: ./alfuc.pdb
> total atoms in file: 23
>> check a
> Checking 'a'....
> Checking parameters for unit 'a'.
> Checking for bond parameters.
> Checking for angle parameters.
> Could not find angle parameter: H1 - CT - OH
> Could not find angle parameter: CT - OH - HO
> Could not find angle parameter: OH - CT - CT
> Could not find angle parameter: H1 - CT - OH
> Could not find angle parameter: H1 - CT - CT
> Could not find angle parameter: CT - OH - HO
> Could not find angle parameter: CT - CT - H1
> Could not find angle parameter: CT - CT - OH
> Could not find angle parameter: OH - CT - CT
> Could not find angle parameter: H1 - CT - OH
> Could not find angle parameter: H1 - CT - CT
> Could not find angle parameter: CT - OH - HO
> Could not find angle parameter: CT - CT - H1
> Could not find angle parameter: CT - CT - OH
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: H1 - CT - CT
> Could not find angle parameter: H1 - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - H1
> Could not find angle parameter: CT - CT - OH
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: OS - CT - CT
> Could not find angle parameter: OS - CT - H1
> Could not find angle parameter: OS - CT - CT
> Could not find angle parameter: OS - CT - CT
> Could not find angle parameter: H2 - CT - OS
> Could not find angle parameter: H2 - CT - CT
> Could not find angle parameter: CT - OS - CT
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: CT - CT - H1
> Could not find angle parameter: CT - CT - OH
> Could not find angle parameter: HO - OH - CT
> Could not find angle parameter: OH - CT - H2
> Could not find angle parameter: OH - CT - OS
> Could not find angle parameter: OH - CT - CT
> There are missing parameters.
> Unit is OK.
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> What could be the reason for it ?
>
> On Wed, Feb 9, 2011 at 5:08 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> I don't know of a way to do it in leap, but you can use a mol2 (use
>> option 1 in [x|t]leap) made by leap as input for antechamber. Using
>> antechamber, you can make a new prep-file that contains the entire
>> molecule. Then, load that prep file into leap and build the prmtop
>> from there. You might want to alter the residue name in the new prep
>> file.
>>
>> x- or t- leap.input.file looks like:
>> source leaprc.GLYCAM_06
>> m = sequence { ROH 0GA }
>> saveMol2 m m.mol2 1
>> quit
>>
>> for sleap, use similar:
>> set default write14scale on
>> source leaprc.GLYCAM_06
>> m = sequence { ROH 0GA }
>> saveMol2 m m.mol2
>> quit
>>
>> run leap:
>> [x|t|s]leap -f leap.input.file
>>
>> run antechamber:
>> antechamber -i m.mol2 -fi mol2 -o m.prep -fo prepi -at amber
>>
>> If anyone knows a better way to do it, please say.
>>
>>
>>
>> On Wed, Feb 9, 2011 at 10:30 AM, mish <smncbr.gmail.com> wrote:
>> > Hi all:
>> > I have a problem with residue names of GLYCAM force field. I am using
>> this
>> > force field for FEP calculation. Since I am trying to prepare, minimize
>> and
>> > equilibrate the system using GLYCAM force field in AMBER and afterword I
>> > will jump to something else. My problem is I need same (only one) residue
>> > name for sugar molecules. In glycam it uses a different residue name for
>> > ring atoms and for -OH group or -OCH3 group. Like for the transformation
>> of
>> > the molecule from me-alpla-L-fucoside (OME for -OCH3 and ofA for fucose
>> > ring) to alpha-L-fucoside (ROH for -OH and 0fA for fucose ring) I want
>> the
>> > amber parameter files having same ATOM names. I found it difficult to
>> edit
>> > the topology file.
>> >
>> > Is it possible for leap to read the PBD file with proper amber naming
>> > convention and then edit the atom/residue names, to make them same, in
>> leap
>> > and write the parameter file ?
>> > or where can we try to change it in written parameter file ?
>> >
>> > Sincerely
>> > mish
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Feb 09 2011 - 10:00:04 PST
