You are welcome Zhicheng. Chandan, please pull the latest changes in votca.csg, Christoph has corrected the issue in csg_call.
--- Sikandar On Wed, Nov 13, 2013 at 12:00 AM, 郭志成 <[email protected]> wrote: > Hi Sikandar: > You are right. I made some mistakes about the parameters for potential > conversion to espresso potential tables. > It is working now based on youre suggestion. Thank you very much! > Best Wishes! > Zhicheng > > > 2013/11/13 Sikandar Mashayak <[email protected]> > >> 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 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. 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