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.
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Thu Aug 22 2013 - 05:30:03 PDT
