Hi Mark,
Using -rtpres also doesn't work.
Since this happens only with a specbond.dat present there could be a
note when using specbond.dat.
Since usually mixed residues (looking for BGLE atoms in BGLM rtp) should
not occur when this fatal error is thrown (?), a more specific
alternative might be to have an additional check for mixed residues and,
in case, an additional warning to the fatal error (like in the case of
missing hydrogen).
Best,
Joerg
On 15.08.2013 18:07, Mark Abraham wrote:
It's not clear whether this is or should be an intended behaviour.
There are lots of considerations of atom and residue renaming that
pdb2gmx tries to handle, and it is not too surprising that there are
corner cases that don't work as everyone expects. I couldn't even find
the code where this might happen. You might have been able to avoid
renaming your .rtp entries manually by using pdb2gmx -rtpres.
Where would have been a good place for you to have read "Using
three-letter .rtp residue names might make life easier. Consider using
pdb2gmx -rtpres if you need longer names."
Mark
On Thu, Aug 15, 2013 at 3:45 PM, Joerg Sauter <joerg.sau...@mpikg.mpg.de> wrote:
Hi,
I am building a tetramer of beta(1-4) linked glucose with pdb2gmx (Gromacs
4.6.3). I have three residue types BGLB BGLM BGLE defined in the
aminoacids.rtp with which I want to built the chain BGLB BGLM BGLM BGLE.
Using pdb2gmx works fine, until I link the residues via the specbond.dat
file:
3
BGLB O4 1 BGLM C1 1 0.147 BGLB BGLM
BGLM O4 1 BGLM C1 1 0.147 BGLM BGLM
BGLM O4 1 BGLE C1 1 0.147 BGLM BGLE
In this case I get the error message:
Fatal error:
Atom HO4 in residue BGLE 4 was not found in rtp entry BGLM with 21 atoms
while sorting atoms.
Using the -debug 1 mode I found that internally (in the chain.pdb) the
residue names get shortened to BGL thus making the residues
indistinguishable. Therefore, pdb2gmx seems to mix up residues resulting in
the error above. If I use residue names consisting of only 3 characters
everything works fine again.
Is this behaviour known or intended? I could not find any note on this in
the manual and it took me some time to figure this out, so maybe there
should be at least a warning.
Best,
Joerg
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Joerg Sauter
Max Planck Institute of Colloids and Interfaces
Department of Theory & Bio-Systems
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