Please include the full error message and the grompp line you used when asking for help. Without them I can't tell what you are doing.
Richard On 04/04/2013 17:40, "라지브간디" <ra...@kaist.ac.kr> wrote: > >Dear Richard, > >I've included the COM in my .gro and also updated the rtp, atp and >ffnonbonded.itp files as well as the exact coefficient value. But when I >use gromp I get the error that COM not found in atom type database . > >Actually I included the COM in atomtypes.atp like >COM 0.0000 > >As it doesn't have mass value. In addition, I included in ffnonbonded. >Itp file by setting their LJ value as 0 ( both sigma and epsilon ) > >Please suggest how to avoid this error. >Thanks in advance. > >Rajiv > > > >Dear Rajiv, > >The .itp looks fine to me except for the coefficient in the virtual site >which I think should be much closer to 0.5. > >If the issue is that you don't have the coordinate on the COM in your >.gro >file then you will need to generate it yourself. If you have one CO >molecule which you use to build a box usingsay genconf I would suggest >just working out the position by hand and modifying the .gro manually. If >that is not the case (ie. you have many CO molecules at all stages of the >process) it's time to get out your favourite programming language and >write a program which reads a .gro and adds the COM to each molecule and >writes it out again. > > >Richard > >On 29/03/2013 06:41, "" wrote: >>Dear Richard, >>For instance, To simulate the hemoglobin with heme ligated CO, would >>like >>to set the charges on center of mass of CO. >>How do i include the virtual sites atom in co-ordinates (x,y and z)?. I >>added the virtual sites line in topology as follows: >> >>[ moleculetype ] >>; molname nrexcl >>CMO 2 >> >> >>[ atoms ] >>; id at type res nr residu name at name cg nr charge >>1 OM 1 CMO O 1 -0.85 15.9994 >>2 CM 1 CMO C 1 -0.75 12.0110 >>3 COM 1 CMO M 1 1.60 0.000 >> >> >>[ bonds ] >>; i j funct length force.c. >>1 2 1 0.1128 933032.0 >> >> >>[ virtual_sites2 ] >>; Vsite from funct a >>3 1 2 1 0.5000 > >> >> >> >> >> >> >>Also, i entered in .atp and .rtp file. Could you please give some >>procedure to do this? Thanks in advance. >> >> >> >> >>Dear Rajiv, >> >>Without a clear explanation of what you are doing and the specific error >>message from grompp it is impossible to offer any sensible advice. >> >>Other pieces of information which might be useful would be, the topology >>file, the actual grompp line, and the gro file for a single CO molecule >> >>Richard >> >>On 28/03/2013 20:02, "������������������������������" wrote: >> >>>Dear gmx, >>> >>>I would like to set virtual sites for CO molecules with some specific >>>charge. >>> >>>As per GROMACS manual, I've created virtual site2 in topology file for >>>CO. Also, given the information in .rtp file as well as added the >>>COM(center of mass) atom in .gro file. However, when I use gromp, it >>>shows COM not found. >>> >>>Please need an advice. Thanks. >>> >>>Rajiv >> > > >------------------------------ >
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