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On 12/25/2011 7:56 PM, Ashalatha Sreshty wrote:
<blockquote
cite="mid:CANV=m+_ztUW1qNBG9d1w2a+5H=sxWb=z1U61gNBRmvEGW4gPVw@mail.gmail.com"
type="cite">Dear All,<br>
<div class="gmail_quote">
<div class="gmail_quote">
<br>
I have a problem running gromacs for a oligosaccharide. it has
14<br>
units sugars containing glucose, mannose and N-acetyl
glucosamine<br>
units. I want to do MD simulations for this with opls aa force
field.<br>
For this I have generated the .itp files using topolgen
(edited the<br>
atoms according to the opls atoms types) but when I am
executing<br>
grompp command the following error comes up:<br>
<br>
ERROR 226 [file 901opls.itp, line 2897]:<br>
No default Ryckaert-Bell. types<br>
</div>
</div>
</blockquote>
<br>
The R-B dihedral defined on line 2897 does not have parameters
associated with it on that line, and grompp could find none for the
atom types involved back in the [dihedraltypes] section of the force
field. You'll have to do some detective work to find out why.<br>
<br>
<blockquote
cite="mid:CANV=m+_ztUW1qNBG9d1w2a+5H=sxWb=z1U61gNBRmvEGW4gPVw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div class="gmail_quote">
ERROR 227 [file 901opls.itp, line 2902]:<br>
No default Ryckaert-Bell. types<br>
ERROR 228 [file 901opls.itp, line 2903]:<br>
No default Ryckaert-Bell. types<br>
ERROR 229 [file 901opls.itp, line 2904]:<br>
No default Ryckaert-Bell. types<br>
<br>
Excluding 3 bonded neighbours molecule type 'DRG'<br>
<br>
NOTE 1 [file 901opls.top, line 19]:<br>
System has non-zero total charge: -2.177100e+01<br>
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</blockquote>
<br>
You have a net charge of -21.771, so your topologies are mangled
somehow.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CANV=m+_ztUW1qNBG9d1w2a+5H=sxWb=z1U61gNBRmvEGW4gPVw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div class="gmail_quote">
<br>
processing coordinates...<br>
double-checking input for internal consistency...<br>
renumbering atomtypes...<br>
converting bonded parameters...<br>
<br>
There was 1 note<br>
<br>
------------------------------
<div class="gmail_quote">-------------------------<br>
Program grompp_d, VERSION 4.0.5<br>
Source code file: grompp.c, line: 986<br>
<br>
Fatal error:<br>
There were 229 errors in input file(s)<br>
<br>
These are the lines of the dihedrals in .itp file <br>
<br>
I do not understand what to do next. Please help me resolve
this problem<br>
and also educate me how to assign opls forcefield to
carbohydrates for<br>
MD simulations. Thank you in advance.<br>
<br>
AshaLatha Sreshty<br>
Molecular Sciences Laboratory<br>
National Institute of Immunology<br>
New Delhi, India</div>
<br>
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<br>
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<br>
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