Dear Amber users,
I simulate a protein ligand system. The ligand is an organic molecule and i
calculated the ESP charge for the ligand using gaussian. After successful
simulation, now i want to calculate mmgb(pb)sa decomposed energy. The
ligand molecule is a single residue, however i want to split the ligand
into multiple residues (suppose i want to split one methyl group as one
residue and rest of the molecule another residue) and calculate the
decomposition energy. Is there any way to do this?
If i only change the residue number in the pdb and create the topology
file, it is giving the following error. Please guide me.
*ERROR: Comparing atoms*
* .R<MOL 358>.A<C30 92>, *
* .R<MOL 1>.A<H4 2>, *
* .R<MOL 1>.A<H5 3>, and *
* .R<MOL 1>.A<H6 4> *
* to atoms*
* .R<MOL 1>.A<C4 5>, *
* .R<MOL 358>.A<C30 92>, *
* .R<MOL 1>.A<H6 4>, and *
* .R<MOL 1>.A<H4 2> *
* This error may be due to faulty Connection atoms.*
*!FATAL ERROR----------------------------------------*
*!FATAL: In file [chirality.c], line 142*
*!FATAL: Message: Atom named C4 from MOL did not match !*
*!*
*!ABORTING.*
Thank you in advance
Rajeswari A,
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Received on Thu Feb 13 2014 - 05:30:03 PST
