Yeah. I select none for the terminal residues.
Gromacs was compiled by myself. I have used this version in production
runs for the last 5 months.
Cheers
Mitch
Justin A. Lemkul wrote:
Sorry, clicked 'send' too soon. How was this version of Gromacs compiled? I
remember submitting a bugzilla not too long ago about a similar problem, and it
ended up being that the Ubuntu package was broken. Re-compiling from source
fixed the problem. The -ter response was a knee-jerk reaction, as a related
problem is somewhere in the list archive.
-Justin
Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
Quoting [EMAIL PROTECTED]:
Hello all,
I have a protein with missing N- and C- terminus residues. I am
simulating a complex. To avoid in-silico charge interactions at the
wrong places due to the missing residues I have performed acetylation
and amidation.
When running pdb2gmx (GMX331) I experience a problem -
pdb2gmx -f blah.pdb -o blah.gro -p blah.top -water spc -ter -ignh -merge
Are you choosing 'none' for your termini?
-Justin
Fatal error:
Atom H not found in residue 177 while adding improper
177 is the number of the NH2 cap after re-numbering of the pdb file.
EXTRACT FROM THE PDB FILE -
.....
ATOM 1382 N NH2 A 181 15.061 41.575 44.283 0.00 0.00
N
ATOM 1383 H1 NH2 A 181 14.812 41.813 45.232 0.00 0.00
H
ATOM 1384 H2 NH2 A 181 16.038 41.447 44.027 0.00 0.00
H
....
The ffG53a6.rtp has the NH2 as -
[ NH2 ]
[ atoms ]
N NT -0.83 0
H1 H 0.415 0
H2 H 0.415 0
[ bonds ]
N H1 gb_2
N H2 gb_2
-C N gb_9
[ angles ]
-O -C N ga_33
-CA -C N ga_19
-C N H1 ga_23
-C N H2 ga_23
H1 N H2 ga_24
[ dihedrals ]
-CA -C N H1 gd_14
[ impropers ]
-C -O N -CA gi_1
N H H -C gi_1
Am I missing something?
I reproduce this error with GMX332.
However, if I use pdb2gmx with v3.2.1, pdb2gmx does not complain !
Does anyone have any ideas/fixes?
Cheers
Mitch
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
_______________________________________________
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