Sorry for that. Here are the types. atom type C1 CC3162 O4 OC311 C4 CC3161 C5 CC3163 C3 CC3161 H4 HCA1
I checked them, but I was not able to find the exact combination of atoms angles and dihedrals associated with them in the ffbonded.itp. For example, I did not find C4-O4-2C1 (CC3161 OC311 CC3162) there, but I found both CC3161 CC3162 OC311 CC3162 CC3161 OC311 > On May 24, 2017, at 11:39 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > On 5/24/17 11:35 AM, Mohammad Hassan Khatami wrote: >> >>> On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami <mhk...@mun.ca >>> <mailto:mhk...@mun.ca>> wrote: >>> >>> Some how I figured out the problem and fixed it! I changed "O4 +C1" to >>> "O4 2C1” and it worked. I hope it is correct. >> Nope! the bond are not made this time! That’s why grompp did not complain! > > That's because CHARMM and GROMACS use different syntax. CHARMM patches use 1 > and 2 to denote the first and second residues supplied in the patch call in > the input script. You can't do the same thing in GROMACS. + and - are to > specify next and previous residue in the .rtp, respectively. pdb2gmx will > silently accept nonexistent atoms like 2C1 because a +/- designator may exist > in a terminal residue, in which case the atom won't be found. > > Your previous message is also not what I asked for. I know what the atom > names are, and I know what the atom types should be, but I don't know what > *types* you actually ended up with in the topology. Please provide the > *types* corresponding to the lines that generate errors. > >>> Now I have to move on to make the more complicated form of my polymer, and >>> add 1->6 connection to the system, like below: >>> >>> 1->6 —AGLC—1->4—AGLC. >>> / >>> AGLC—1->4—AGLC—1->4—AGLC >>> >>> Now I will rename the residues, based on their position as follow: >>> >>> 1->6 —AGM—1->4—AGF >>> / >>> AGI—1->4—AG6—1->4—AGF >>> >>> Now, I am a bit confused. This time AG6 is going to be connected to AGF >>> trough 1->4 bond, which I will add it to the residue using "O4 2C1” >>> (which I will do similar to what I did before), but for the 1->6 connection >>> to AGM, I would need to connect O6 of AG6 to C1 of AGM. Should I connect >>> it through bond O6 3C1? or O6 2C1(which would be odd!)? >>> > > You can do branching with specbond.dat entries (see the manual) but GROMACS > has difficulty with this. It is trivial to perform in CHARMM. > > -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
