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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