[gmx-users] grompp erro
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?
> 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.
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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