On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
I used 13. GROMOS 53a6 force field
"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input."
So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu)
I get the following options.
Which GLUTAMIC ACID type do you want for residue 1
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)
Both options give the same error as before.
The same error occurs for HB1 as well.
Will I have to edit the pdb or rtp file? Or any other suggestions?
Read the error message again; it tells you what to do.
Consider what you're doing - you're supplying a united-atom force field with an
all-atom structure. The chosen parameter set doesn't have explicit hydrogens on
nonpolar groups. Hence pdb2gmx complains that you're giving it atoms it doesn't
understand. Use of -ignh solves this issue, which is precisely what the error
message is telling you.
-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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
