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<div class="moz-cite-prefix">Hi,<br>
<br>
i think this is an unknown issue. It probably only shows up with
the GROMOS force field, since all other force fields supplied with
Gromacs have an HS atom type. It would indeed be better to
automatically determine the constraint length for the bond lengths
and the angle. But I don't know if we can do this, since this
would also auto-generate parameters for other topologies where,
maybe, this is not desirable.<br>
<br>
I created a redmine issue:<br>
<a class="moz-txt-link-freetext" href="http://redmine.gromacs.org/issues/1422">http://redmine.gromacs.org/issues/1422</a><br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 01/15/2014 06:55 AM, Karmen Condic-Jurkic wrote:<br>
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Hi everyone,
<br>
<br>
<br>
I'm a new Gromacs user and I bumped into a problem with the
parameter assignment to the constraint bonds in COH and CSH
groups in serines and cysteines when flag
<i>-vsite hydrogens</i> is being used in the topology
preparation. Namely, after running an energy minimisation on the
system built with virtual sites, I noticed that CSH angles in
cysteines ended up with a strange pointy form corresponding to
75 degrees, instead of the equilibrium value of 96. After a bit
of a digging, it turned out that the problem is created during
the grompp run, where only a single function is created to
represent the constraint bond that prevents angle bending for
both COH and CSH groups. There parameter used in that particular
function corresponds to the COH group (0.198 nm), which is too
short for CSH (should be 0.237 nm) and results with the
distorted CSH angle. The reason why this happens seems to be the
vague definition of the constraint bond given through the atom
types (CH2 and H), which are unfortunately the same for both CYS
and SER. In addition,
<font face="Tahoma" size="2" color="black"><span
style="font-size:10pt;" dir="ltr">the CH2-H distance
parameter for CSH is actually completely omitted from the
current ffG54a7bon.file!
</span></font>There is no problem with other COH groups, which
are defined through different atom types, as shown below in the
excerpt from ffG54a7bon.itp file with parts of interest
highlighted:<br>
<br>
<font face="Tahoma" size="2" color="black"><span
style="font-size:10pt;" dir="ltr">*************************************************************************<br>
; get the constraint distances for dummy atom constructions<br>
<br>
#include "ff_dum.itp"<br>
<br>
[ constrainttypes ]<br>
; now the constraints for the rigid NH3 groups<br>
MNH3 C 2 DC_MNC1<br>
MNH3 CH1 2 DC_MNC2<br>
MNH3 CH2 2 DC_MNC2<br>
MNH3 MNH3 2 DC_MNMN<br>
; and the angle-constraints for OH and SH groups in
proteins:<br>
<span style="background-color:#FFCC99;"> CH2 H 2
DC_CO</span><br>
CH1 H 2 DC_CO<br>
C H 2 DC_CO<br>
P H 2 DC_PO<br>
<span style="background-color:#FFCC99;">
????????????????????? missing DC_CS value</span><br>
**************************************************************************</span></font><br>
<br>
I'm not really sure if this belongs to the developers or to the
users mailing list, but I gues that depends on the solution of
the problem. It can be probably done on a more general level by
redefining the constraints using more unique atom descriptors or
just by calculating the atom distance for each constraint of
interest by looking at the atoms directly and not reading in a
fixed value. As I have no experience in coding in C, this goes
way beyond my programming skills so I came up with an easier
solution - introducing additional atom type for hydrogen bound
to sulphur named HS. With this, the grompp was able to override
this issue and this seems to be working:<br>
<br>
<font face="Tahoma" size="2" color="black"><span
style="font-size:10pt;" dir="ltr">**************************************************************************<br>
; get the constraint distances for dummy atom constructions<br>
<br>
#include "ff_dum.itp"<br>
<br>
[ constrainttypes ]<br>
; now the constraints for the rigid NH3 groups<br>
MNH3 C 2 DC_MNC1<br>
MNH3 CH1 2 DC_MNC2<br>
MNH3 CH2 2 DC_MNC2<br>
MNH3 MNH3 2 DC_MNMN<br>
; and the angle-constraints for OH and SH groups in
proteins:<br>
<span style="background-color:#FFCC99;"> CH2 H 2
DC_CO</span><br>
CH1 H 2 DC_CO<br>
C H 2 DC_CO<br>
P H 2 DC_PO<br>
<span style="background-color:#FFCC00;"> CH2 HS 2
DC_CS</span><br>
<br>
************************************************************************<br>
<br>
<br>
I duplicated all the parameters given for atom type H and
reassigned them to HS type. The modified force field files
(version G54a7) are in the attachment and have suffix _HS.<br>
<br>
I was trying to find if this problem was already known, but
I couldn't find anything related to this issue. In any case,
it would be good to fix this as many proteins contain
cysteines, but in case it has already been fixed, I
apologize for spamming.<br>
<br>
All the best, <br>
<br>
Karmen<br>
<br>
</span></font>
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<div><font face="Tahoma" size="2"><br>
-----------------------------<br>
Dr. Karmen Condic-Jurkic</font><font
face="Tahoma" size="2"><span class="signature"><br>
Postdoctoral Researcher <br>
School of Chemistry and Molecular Biosciences<br>
The University of Queensland</span></font><font
face="Tahoma" size="2"><span class="signature"><font
face="Tahoma" size="2"><span
class="signature"><br>
</span></font>Brisbane<font size="2"> St.
Luc<font size="2">ia, </font>QLD</font> 407<font
size="2">2<br>
Aus<font size="2">tralia</font></font> </span></font></div>
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