Hi,
You may be able to fix this via parmed. First use the 'checkValidity'
command to make sure there are no other issues. If not, a correct
ATOMS_PER_MOLECULE section can be set with 'setMolecules'.
Hope this helps,
-Dan
On Thu, Feb 11, 2016 at 12:56 PM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
> Dear All,
>
> I am simulating a system of two sugar molecules in water box. I obtain the structure from glycam website, and bind monosaccharides using bond command in tleap. When running equilibration run, a faced with the error “Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM”. Interestingly (for me, at least), both minimization and heating runs did not give any errors, although I am using sander.MPI for all pre-production runs.
>
> I know this is a known bug in tleap, and also know how to fix it. I wanted to ask if it would be safe to think that bond command worked correctly when I do not get any “bad topology” errors.
>
> With the same bond commands in tleap I have created many systems, and this is the first time that I got such an error.
>
> I use AmberTools15, if it helps.
>
> Best,
> Batuhan
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Feb 11 2016 - 12:30:03 PST
