Editing CT to CG is what makes sure you get Glycam06 params. CG is
the atom type used by Glycam to specify "glycan carbon." That
procedure should give you exactly the same parameters.
On Tue, Apr 5, 2011 at 1:05 PM, mish <smncbr.gmail.com> wrote:
> Thanks ..yes this was the mistake.
> I want to ask one more thing that the prm file in this case have exactly
> same GLYCAM_06 parameters or not ? Is this editing of CT to CG id not
> effecting the parms ?
>
>
>
> On Tue, Apr 5, 2011 at 6:46 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> I just got it all to work. So... One possible answer... did you name
>> the pdb file MFU and the prep file mfu? Residue names in leap are
>> case sensitive.
>>
>>
>> On Tue, Apr 5, 2011 at 12:20 PM, mish <smncbr.gmail.com> wrote:
>> > I tried it in the way you mentioned before, but still there is some
>> mistake
>> > I am doing, which I can figure out.
>> >
>> > 1- tleap input file is :
>> > source leaprc.GLYCAM_06
>> > mfu = sequence { OME 0fA }
>> > saveMol2 mfu mfu.mol2 1
>> > quit
>> >
>> > 2- Edited residue name to MFU for whole residue and changed the residue
>> > number to 1.
>> >
>> > 3- Then I ran the antechamber to get prep file :
>> > antechamber -i mfu.mol2 -fi mol2 -o mfu.prep -fo prepi -at amber
>> >
>> > 4- Changed atomtype CT to CG in mfu.prep
>> >
>> > 5 - loading a pdb file of sequence { OME 0fA } with residue name MFU and
>> > same residue number 1 for all atoms in tleap by file
>> >
>> > source leaprc.GLYCAM_06
>> > loadamberprep mfu.prep
>> > mefuc=loadpdb mfu.pdb
>> > saveamberparm mfeuc mefuc.top mefuc.rst
>> > quit
>> >
>> > I am getting the fallowing error :
>> > -----------------------------
>> >
>> -----------------------------------------------------------------------------------------------------------------------------------
>> >
>> > Loading Prep file: ./mfu.prep
>> > Loading PDB file: ./mfu.pdb
>> > Added missing heavy atom: .R<MFU 1>.A<C2 23>
>> > Added missing heavy atom: .R<MFU 1>.A<C3 19>
>> > Added missing heavy atom: .R<MFU 1>.A<O2 25>
>> > Added missing heavy atom: .R<MFU 1>.A<C1 6>
>> > Added missing heavy atom: .R<MFU 1>.A<C4 15>
>> > Added missing heavy atom: .R<MFU 1>.A<O3 21>
>> > Added missing heavy atom: .R<MFU 1>.A<O5 8>
>> > Added missing heavy atom: .R<MFU 1>.A<C5 9>
>> > Added missing heavy atom: .R<MFU 1>.A<O4 17>
>> > Added missing heavy atom: .R<MFU 1>.A<C6 11>
>> > ERROR: Comparing atoms
>> > .R<MFU 1>.A<O2 25>,
>> > .R<MFU 1>.A<H2 2>,
>> > .R<MFU 1>.A<H3 3>, and
>> > .R<MFU 1>.A<H1 4>
>> > to atoms
>> > .R<MFU 1>.A<O 5>,
>> > .R<MFU 1>.A<O2 25>,
>> > .R<MFU 1>.A<H1 4>, and
>> > .R<MFU 1>.A<H2 2>
>> > This error may be due to faulty Connection atoms.
>> > !FATAL ERROR----------------------------------------
>> > !FATAL: In file [chirality.c], line 140
>> > !FATAL: Message: Atom named O from MFU did not match !
>> > !
>> > !ABORTING.
>> >
>> -------------------------------------------------------------------------------------------------------------------------------------------------------
>> > On Wed, Feb 9, 2011 at 6:39 PM, Lachele Foley (Lists) <lf.list.gmail.com
>> >wrote:
>> >
>> >> 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
>> >>
>> >> _______________________________________________
>> >> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Apr 05 2011 - 11:00:03 PDT
