[gmx-users] special bond

[Justin Lemkul]

On 4/29/14, 10:34 AM, Nicola Staffolani wrote:
> ​"​
> Using ATM1 and ATM2 has no effect in ffbonded.itp
> ​" even if I do have defined ​​"​such atom types" in atomtypes.dat (and
> also in ffnonbonded.itp)?
>

OK, the use of the same name and type is a bit confusing, so it wasn't clear 
from the last post that this should work.  In this case, it should (though of 
course you will get fatal errors regarding missing angles unless you define 
suitable [angletypes], but that's a separate issue).

So the net effect of what you are saying is: pdb2gmx writes the bond between 
ATM1 and ATM2, but does not write gd_99 into the .top as reference to the 
parameters, do I have that correct?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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