Dear Amber users,
I'm simulating some drug-protein complexes (obtained with Autodock) in
order to obtain free energies of binding. I'm using antechamber for obtain
the missing parameters for the small molecules,. The force field I'm using
is ff12SB. Everything works well with the exception of one complex which is
causing me several problems: using as input the coordinate file I obtained
with tleap, I get this error in the output file when I'm trying to minimize
the structure with PMEMD.CUDA:
| ERROR: I could not find enough coordinates in **.inpcrd
moreover when I try to load the topology and the coordinates files in VMD
nothing is appearing on the screen (I selected amber 7 parm for prmtop file
and amber 7 restart for the inpcrd) . There are not errors displayed by
antechamber or VMD, and when I tried to obtain the inpcrd file for the drug
alone, it was empty (while the prmtop file was ok). However the pdb
obtained with tleap for the same complex works perfectly on VMD. I tried
also to obtain a rst file from this pdb using VMD and use it together with
the prmtop for my simulations instead of the inpcrd but it gives me the
following error again in the output file:
| ERROR: nfft1 must be in the range of 6 to 512!
| ERROR: nfft3 must be in the range of 6 to 512!
| ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: alpha must be in the range of 0.30000E+02 to 0.15000E+03!
| ERROR: beta must be in the range of 0.30000E+02 to 0.15000E+03!
| ERROR: gamma must be in the range of 0.30000E+02 to 0.15000E+03!
Input errors occurred. Terminating execution.
I don't know what I'm doing wrong as the scripts that I'm using for
preparing and simulating my complex are the same I used for the other
complexes (that were already prepared and simulated without any problem).
I'm guessing that there is something wrong with the small molecule but as I
said before no errors were displayed during the preparation phase and the
structure looks ok. I already tried to rebuild the drug and re dock it in
Autodock, but nothing is changed. I really appreciate if someone could help
me with this issue. Many thanks, best regards
Francesco Gentile
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 16 2014 - 11:00:03 PDT
