[gmx-users] grompp erro

Justin Lemkul jalemkul at vt.edu
Tue Jan 21 15:59:01 CET 2014

On 1/21/14, 3:13 AM, Albert wrote:
> On 01/21/2014 12:46 AM, Mark Abraham wrote:
>> Why are you trying to make a methylated amine into an NH2 via your choice
>> of 1 for -ter?
>> Mark
> yes, for the c-term. I delete the frist residue Thr from my pdb file, and the
> problem solved. It seems that this error related the Thr at n-term.

There are a couple of missing [angletypes] in our ports.  It appears the 
CHARMM27 files were manually modified with some additional parameters inserted 
to cover such cases.  Specifically, NH2-CT1-CT1 and NH2-CT1-CT3 types are 
missing, so if anyone has Thr, Ile, or Ala at the N-terminus and chooses a 
neutral (-NH2) terminus, the error will come up.

We'll fix the ports sometime soon, but in the meantime, you can use the bonded 
parameters for those angles from charmm27.ff/ffbonded.itp.



Justin A. Lemkul, Ph.D.
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


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