Hi Dan,
Thank you for the reply. Yes, I did check via parmed and it showed me the error in the topology file.
I’m not sure if this is relevant but what might be the reason that sander did not complain about the topology while minimising and heating the system, but it halted when the equilibration started?
Batuhan
> On 11 Feb 2016, at 21:07, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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/
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Received on Thu Feb 11 2016 - 12:30:04 PST
