On 6/27/12 6:38 AM, Shima Arasteh wrote:
I added this line to the residuetypes.dat file:
FOR Protein
Then running this command:
pdb2gmx -f protein.pdb -water spc -ter
Written as blow:
Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
Asked for terminus:
I chose "none" as the N-terminus.
Getting this:
Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for VAL-1
0: NH3+
1: NH2
2: None
2
Start terminus VAL-1: None
Select end terminus type for GLY-24
0: COO-
1: COOH
2: None
0
End terminus GLY-24: COO-
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file:
/home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper
terminal entry.
Would you helping me with it with your useful suggestions?
I honestly have no idea why that's not working. It's the exact same workflow
used with all other capping groups and I use it routinely.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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