Dear Francois, Dac,
The problem is, as I capped the monomers while optimization in gaussian,
so the unit of monomer
has the capped atoms and leap is adding those atoms to the structure as I
have to mention the
residue name in pdb file. How to deal with these capped atoms to get a
structure with the build pdb in xLeap
and the optimized monomers.
> Thisnis wrong: leap is only comparing atom *names* between the pdb file
and the library
file
Sorry, I also mean the same while comparing atom names its giving the
following error in leap.log file
*ERROR: Comparing atoms
*
*.......*
*....*
* This error may be due to faulty Connection atoms.*
*
*
Finally xLeap is crashing with the following
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named S1 from CA did not match !
!
!ABORTING.
On Fri, Aug 23, 2013 at 9:17 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Joshi,
>
> > I capped the monomer and get the monomer prep file and libraries using
> > antechamber.
> > Now when I load pdb file build in xLeap with these monomer libraries, it
> > compares both
> > monomer (i.e. one in pdb file and other in optimized prep file), and find
> > the mismatch.
>
> the match between the FF lib and the PDB file occurs only if the same
> atom and residue names are found in the FF lib and PDB file... if
> missing atoms are found in the PDB file there are added based on what
> is found in the FF lib.
>
> > Since antechamber gave the different atom types to the atoms,which is not
> > matching to the
> > pdb structure generated before, its creating Leap error. Any idea to get
> > over this.
> >
> > May be this vague way of doing this but I couldn't find any smarter way
> of
> > doing this.
> > If anyone has done this before, kindly let me know. I have seen people
> > reported PNA
> > simulation in similar way in AMBER.
>
> PNA for peptide nucleic acid?
> See http://q4md-forcefieldtools.org/REDDB/projects/F-93/ by J. Sanders
>
> regards, Francois
>
>
> > On Thu, Aug 22, 2013 at 5:49 PM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >
> >> Dear Joshi,
> >>
> >> > I want to set up topology and coordinate file to set up an amber
> >> > simulation for a new structure. I build the polymer in xLeap and get
> pdb
> >> > structure . To get a valid charges and geometry, I optimized the
> monomers
> >> > in gaussian and got amber prepin and frcmod file for this monomer.
> >>
> >> This procedure is rather vague: In general the monomers are capped and
> >> from capped monomers molecular fragments are generated. Then FF
> >> libraries generated for these FF fragments are associated in the LEaP
> >> program to match the structure of the polymer provided to the PDB file
> >> format.
> >>
> >> Which tool did you use to do that? Doing that manually is quite
> >> error-prone...
> >>
> >> > Now I want to use these monomer parameters and charges to my
> previously
> >> > build xLeap polymer structure. Here are two issues
> >> >
> >> > 1. How can I edit the charges of previous atoms to new optimized
> atoms,
> >> > using the *edit selected atoms* in xLeap its very much time taking.
> >>
> >> What do you want to edit the charges? in general the charges are
> >> available in a force field library that is loaded in LEaP; so no need
> >> to 'edit' the charges. You just need to load the FF library
> >> (mol2/mol3, off or prep file format) generated by the tool you used.
> >>
> >> > 2. I added some hydrogen in the structure, and xLeap is not
> recognizing
> >> the
> >> > atoms with the following error,
> >>
> >> A FF lib has to contain the hydrogen atoms; on the contrary the
> >> hydrogens do not need to be present in the PDB (polymer) file; they
> >> will be automatically added by LEaP if a match is found between each
> >> residue in the PDB file and the FF libs.
> >>
> >> regards, Francois
> >>
> >>
> >> > If there is some tutorial or technique, kindly refer me to the same.
> >> > *Unit Editor: FATAL: Atom .R<DA 2>.A<H33 33> does not have a type.*
> >> > *
> >> > *
> >> > If there is some tutorial or technique, kindly refer me to the same.
> >> > Thanks in advance.
> >>
>
>
>
>
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>
--
*With Regards,
HIMANSHU JOSHI
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
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Received on Mon Aug 26 2013 - 22:30:03 PDT
