[gmx-users] grompp erro
jalemkul at vt.edu
Sun Jan 19 21:08:23 CET 2014
On 1/19/14, 12:03 PM, Albert wrote:
> thanks a lot for kind reply.
> Now I noticed that this comes from the terminal residues after I further
> confirmed and repeated it again instead of protonated residues.
> I run: pdb2gmx -f mae.pdb -ignh -o test.pdb -ter
> Select start terminus type for THR-19
> 0: NH3+
> 1: NH2
> 2: 5TER
> 3: None
> Start terminus THR-19: NH2
> Select end terminus type for CYS-322
> 0: COO-
> 1: COOH
> 2: CT2
> 3: 3TER
> 4: None
> if I don't add option "-ter", this error doesn't happen.
That still doesn't provide anything more useful than before. Please answer the
questions I posed in my last message. The essential information is on line
23560 of the problematic topology.
> On 01/19/2014 05:41 PM, Justin Lemkul wrote:
>> All of this is critical information that you left out of your original post,
>> hence my assumption that your issue could be easily solved. When reporting a
>> problem, please be as specific as possible! If there is a problem with our
>> latest parameters, we need to fix that, but I don't yet have enough
>> information to tell you what's wrong. grompp did, however, give you what you
>> need to figure it out. The fatal error comes from line 23560 of the topology
>> file. What is on that line? What are those atoms and what are their types?
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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