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
1
Start terminus THR-19: NH2
Select end terminus type for CYS-322
0: COO-
1: COOH
2: CT2
3: 3TER
4: None
1
if I don't add option "-ter", this error doesn't happen.
best
Albert
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
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
