Thank you for your prompt response. I have attached the cgtop.top file. I was trying to figure out what to add to the . top file and added the [defaults] segment. The initial output from csg_gmxtopol started from [moleculetype]. Thanks again.
On Wednesday, 24 May 2017 17:08:13 UTC-4, Christoph Junghans wrote: > > 2017-05-24 14:11 GMT-06:00 M. Chakraborty <[email protected] > <javascript:>>: > > I am trying to use the tabulated potential (for non-bonded interactions) > > obtained from force-matching to run coarse-grained simulation in > gromacs. To > > obtain the topology file I have used csg_gmxtopol. conf_cg.gro file was > > obtained by running csg_map. In order to use the tabulated potential for > > simulation, I have made the following changes to the mdp file: > > vdwtype = User > > coulombtype = User > > energygrps = A B > > energygrp_table = A A B B > > > > > > I must mention here that I have mapped methanol molecules into > > coarse-grained particles having two beads representation (A for CH3 and > B > > for OH). When I run the command, gmx grompp -v -f cg_grompp.mdp -p > cgtop.top > > -c conf_cg.gro, I get the following error: > > Fatal error: > > Syntax error - File cgtop.top, line 4 > > Last line read: > > '[ moleculetype ]' > > Invalid order for directive moleculetype > > > > I am not sure what is going on here. I am attempting to run a > coarse-grained > > simulation for the first time. It would be really helpful if someone can > > guide me to identify what is wrong with my approach. > The output of csg_gmxtopol is only meant as a template and "File still > needs to be modified by the user" (from --help output). > > Can you post your cgtop.top and we might be able to help? > > Christoph > > > > > Thank You. > > > > M. Chakraborty > > > > -- > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
cgtop.top
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