Hi Francois and Dac,
I used TER to separate to residues in pdb and the error of Comparing atoms
has cure,
now I am modifying the pdb atom name and hope it will work.
Thanks a lot for valuable inputs.
On Tue, Aug 27, 2013 at 10:34 AM, HIMANSHU JOSHI <himanshuphy87.gmail.com>wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> *With Regards,
> HIMANSHU JOSHI
> Graduate Scholar, Center for Condense Matter Theory
> Department of Physics IISc.,Bangalore India 560012*
>
--
*With Regards,
HIMANSHU JOSHI
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
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Received on Tue Aug 27 2013 - 06:00:03 PDT
