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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Received on Fri Aug 23 2013 - 09:00:04 PDT
