Hi I am sorry I was not clear in my response.
The reason for the errors was that the table.xml file provided by you did not contain all the required parameters for potential conversions to espresso potential tables. Also, the sequence of parameters inside the table.xml file was not right. I have corrected the table.xml file, which is attached below. May be you can compare it with earlier settings to understand what was going wrong. I hope this helps. Cheers Sikandar On Thu, Nov 7, 2013 at 3:14 AM, 郭志成 <[email protected]> wrote: > Hi > > Thanks for your suggestion. For your comment, however, it is the method of > calculating the coarse-grained potential using ibi procedure by espresso > soft. I have obtained the coarse-grained potential (CG-CG.pot) calculated > by gromacs with ibi procedure. I want to convert this potential to espresso > format using csg_call convert_potential espresso. Anyway, thanks again for > your reply. > > 2013/11/7 Chandan Choudhury <[email protected]> > >> >> On Wed, Nov 6, 2013 at 9:32 PM, Sikandar Mashayak >> <[email protected]>wrote: >> >>> Hi >>> >>> I am trying to reproduce the error, but when I run the same command >>> 'csg_call --options table.xml --ia-type non-bonded --ia-name >>> CG-CG convert_potential espresso CG-CG.pot tab', the command just get stuck >>> and I am not getting any error or any kind of output. >>> >>> I am not sure why is csg_call getting stuck. >>> >> >> Hi Sikandar, >> >> I second your observation. >> This behavior is true for the 1.3-dev version. But if I try it on 1.2.3 >> it executes. As I need to toggle between the two versions, this was never a >> problem for for me. >> >> Chandan >> >>> >>> Anyway, I guess, issue of property 'max' not found is due to incomplete >>> information in table.xml. Try using the settings.xml given in ibi_esspresso >>> tutorial instead of your table.xml. I hope that should work well. >>> >>> -- >>> Sikandar >>> >>> >>> On Wed, Nov 6, 2013 at 2:46 AM, Zhicheng <[email protected]> wrote: >>> >>>> Hi Christoph: >>>> >>>> Thanks for your reply. I use the 'csg_call --options table.xml >>>> --ia-type non-bonded --ia-name CG-CG convert_potential espresso CG-CG.pot >>>> tab' to convert the coarse-grained potential(CG-CG.pot) calculated by >>>> gromacs ibi procedure to espresso format(tab). However, I get the following >>>> error message: >>>> >>>> >>>> csg_get_interaction_property: Could not get 'max' for interaction with >>>> name 'CG-CG' >>>> from table.xml and no default was found in >>>> >>>> >>>> /home/adminuser/votca_ctp/share/votca/xml/csg_defaults.xml Details can be >>>> found above . >>>> >>>> >>>> 在 2013年11月6日星期三UTC+8上午12时47分44秒，Christoph Junghans写道： >>>> >>>>> 2013/11/5 郭志成 <[email protected]>: >>>>> > Hi: >>>>> > >>>>> > I convert the csg potential files to the tab format (as read by >>>>> espresso) >>>>> > using table_to_tab.pl (csg_call convert_potential tab). >>>>> > >>>>> > However, it needed three parameters (table_to_tab.sh in_pot >>>>> in_deriv_pot >>>>> > outfile). >>>>> > >>>>> > The problem is that I can not understand the meaning of >>>>> in_deriv_pot. How >>>>> > can I obtain the in_deriv_pot? >>>>> csg_call convert_potential tab is just the low level script, which >>>>> need an extra file with the derivatives in it. >>>>> >>>>> csg_call convert_potential espresso >>>>> should do what you want to do. >>>>> >>>>> > >>>>> > I will be very appreciable for any suggestion. >>>>> > >>>>> > -- >>>>> > You received this message because you are subscribed to the Google >>>>> Groups >>>>> > "votca" group. >>>>> > To unsubscribe from this group and stop receiving emails from it, >>>>> send an >>>>> > email to [email protected]. >>>>> > To post to this group, send email to [email protected]. >>>>> > Visit this group at http://groups.google.com/group/votca. >>>>> > For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>>> >>>>> >>>>> -- >>>>> Christoph Junghans >>>>> Web: http://www.compphys.de >>>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at http://groups.google.com/group/votca. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "votca" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/votca/ueau1mPHG_Q/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> [email protected]. >> >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
<<attachment: CG-CG.pot.cur>>
<cg>
<!-- interaction options for inverse -->
<non-bonded>
<name>CG-CG</name>
<type1>CG</type1>
<type2>CG</type2>
<min>0.0</min>
<max>1.54</max>
<inverse>
<espresso>
<table>table_CG_CG.tab</table>
</espresso>
</inverse>
</non-bonded>
<inverse>
<espresso>
<table_bins>0.005</table_bins>
<table_end>2.45</table_end>
</espresso>
</inverse>
</cg>
