Look at the leap.log for an answer, and compare your PDB to any in the
demos for an idea of what works.
It sounds like a badly-formatted pdb or leap not having libraries loaded.
Bill
On 9/16/20 6:43 PM, Farkhad Maksudov wrote:
> Dear Amber developers and users,
>
> I am trying to create topology and coordinate files for RNA containing
> modifications in ribose sugars of nucleoside. To reach this aim I am
> following recommendations from this tutorial
> https://ambermd.org/tutorials/basic/tutorial4/create_prmtop.htm:
> I calculated partial charges,
> then I obtained missing parameters using parmchk2 utility.
> After that I loaded mol2 file (containing coordinates, charges and residue
> names) and frcmod file into tleap program and using GAFF force field got
> prmtop file for my system. But for some reason in the output topology file
> RNA is represented as only one large residue named "***" instead of a
> number of separate residues (such as A, C, G and U as it is in input mol2
> file).
>
> My question is: Why did tleap put all atoms into one residue? And how can I
> fix my prmtop file or make a new one with the correct number of residues?
>
> Any idea will be appreciated.
>
> Thank you in advance,
> Farkhad
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Received on Wed Sep 16 2020 - 20:30:03 PDT
