Thanks, this very helpful!!!
Sent from my iPhone
On Mar 15, 2009, at 3:48 PM, "Justin A. Lemkul" <[email protected]> wrote:
Tsjerk Wassenaar wrote:
Hi,
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.3
Source code file: pgutil.c, line: 87
Fatal error:
Atom N not found in residue 1094904186 while adding improper
-------------------------------------------------------
This could well be something platform/compiler related. I think it
comes pretty close to the maximum for a signed int.
If I comment out
CA +N C O improper_O_C_X_Y
Right, because if the residue is by itself, there will be no N in
the next residue (+N).
If this is true then pdb2gmx will crash evertime it is run on an
isolated
AA, which it doesn't.
Not if pdb2gmx recognizes how to treat termini. If you are using
non-standard residues and creating new linkages between polymers,
then you
may encounter problems. Perhaps the problem relates the actual
residue
itself, have you added ASBG to aminoacids.dat? You haven't showed
us your
pdb2gmx command line, so we can only assume that something is not
being done
correctly.
This is not correct. Okay, you got me doubt myself a bit, so I tested
and had HOH include a bond from OW to +OW. It's not in either .tdb,
so
according to Justin it would fail by itself. But it doesn't. pdb2gmx
neglects references to other residues if these residues are not
present. So something else is wrong. However, for us to be able to
help, a more complete account of the problem is necessary. The best
thing to do is to send the .rtp entry and the coordinates, if you're
not too sensitive about them being archived while your just working
on
them. Also, do provide details regarding version, platform, shoe size
and anything else that may seem appropriate to diagnose the problem.
Cheers,
Tsjerk
Thanks to Tsjerk for pointing out a mistake on my part. Apologies
for being inarticulate. What I was really getting at was that I
have seen random errors (and not necessarily this one in particular)
resulting from not including amino acids in aminoacids.dat. For
example, I have used some non-standard amino acids in some
simulations and seen similar errors when pdb2gmx did not know they
should be linked like amino acids. So there are two things I'd
suggest considering, in addition to the information that Tsjerk
suggested:
1. Add ASBG to aminoacids.dat
2. Consider whether or not you need to make an entry into
specbond.dat; if the polymer is connected through the side chain as
you initially said, then you may have to define a special bond or
atom name to discern this amide bond from the one present in the
backbone of the amino acid.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
