Hi JiYuan,
You don't need to send your messages to a developer personally, unless otherwise requested. Just the list should suffice.
On 21/11/2011, at 8:05 AM, JiYuan Liu wrote:
> Hi Martin,'
> I have looked for my 3H68_OH_chg1.xml and 3H68_OH_chg1.xml,they have
> atomcharge,you can see in my attachment.When I run the
> 3H68_OH_toAmberFormats_sem.bcl,it genarated the 3H68_OH_chg2.prep that don't
> have the atomcharges.
I'll let Martin handle this one.
> If I setatomtype as setAtomType NAME/AS1/.OD1 NAME/OA in the
> 3H68_OH_sidechain.bcl,could I change the atomname OD1 of 3H68_OH_fixed.pdb
> into OA when I operate loadpdb and saveamberparm procedure?
No. OD1 is an atom name, while OA is an atom type. Any atom needs both those things. For amino acid residues, you're best leaving the atom name alone where possible.
Regards,
Ben
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Received on Tue Nov 22 2011 - 20:00:03 PST
