Hi Everybody,
I am running AF-NMR from Shifts 5.1 on a system with nonstandard residues.
AF-NMR seems to run fine, but the generated pqr and gaussian com files of
the nonstandard residue fragments have duplicate overlapped residues, along
with some lone, grossly misplaced hydrogen atoms. This only occurs for the
nonstandard residues; the standard residues come out properly.
I modified the leap section of the AF-NMR file to accommodate for my
nonstandard residues. ( I have to load in mol2's and a custom frcmod...)
but his does not raise any flags except for a 'pair' flag (which is because
I do not have pair installed), and a shell error.
Running AFNMR on AZU1_NO_H_MIN.pdb
Running tleap
*** Error: tl_getline(): not interactive, use stdio.
Minimization
MS
PBSA
gridprune
/home/teri/CHEM_SOFTWARE/shifts-5.1/bin/afnmr: 384:
/home/teri/CHEM_SOFTWARE/shifts-5.1/bin/afnmr: pair: not found
afnmr.x
done
The prmtop seems to get generated properly and everything seems to work
normally otherwise.. (I have attached a sample pqr file that exhibits
duplication, and the modified afnmr script )
My hunch is that AFNMR.x is not properly generating the nonstandard residue
fragments.
Any advice is appreciated,
Thanks,
Teri
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- application/octet-stream attachment: afnmr
Received on Thu Oct 06 2016 - 19:00:02 PDT
