Hi, Does your input conformation + topology work for a single molecule of this type?
Mark On Sun, Nov 11, 2018 at 1:08 AM Karpurmanjari Kakati < ch18resch01...@iith.ac.in> wrote: > Hi > I tried doing the same, like you said. > 1. Copied the OPLS AA force field files to the directory, where my pdb > files were present. > 2. Modified the rtp file. but the error comes up in the pdb2gmx "no > residjue type in the residue database. " > Alternatively, what I tired doing is the following: > > 1. I constructed the polymer in Avogrado software. > 2. Used OBGMX to make the itp file. But the charge column genereated by > OBGMX is 0000. > 3. To include charge, I went back to Avogrado, and took the charges from > each atom and included it in the itp file by replacing the 0000 against > each atom. > 4. Now my topology file looks something like this: > > > > #include "oplsaa.ff/forcefield.itp" > > > > [ atomtypes ] > ; name1 name2 mass charge ptype sigma epsilon > N_3 N_3 14.0067 0.227 A 0.3261 0.2889 > C_3 C_3 12.0107 0.050 A 0.3431 0.4396 > C_2 C_2 12.0107 0.261 A 0.3431 0.4396 > O_2 O_2 15.9994 -0.013 A 0.3118 0.2512 > N_2 N_2 14.0067 -0.302 A 0.3261 0.2889 > N_R N_R 14.0067 -0.289 A 0.3261 0.2889 > O_3 O_3 15.9994 -0.390 A 0.3118 0.2512 > H_ H_ 1.0079 0.200 A 0.2571 0.1842 > NE NE 14.0067 0.227 A 0.3261 0.2889 > NH1 NH1 14.0067 0.227 A 0.3261 0.2889 > NH2 NH2 14.0067 0.227 A 0.3261 0.2889 > > CA CA 12.0107 0.050 A 0.3431 0.4396 > C C 12.0107 0.050 A 0.3431 0.4396 > CB CB 12.0107 0.261 A 0.3431 0.4396 > CG CG 12.0107 0.261 A 0.3431 0.4396 > CD CD 12.0107 0.261 A 0.3431 0.4396 > CZ CZ 12.0107 0.261 A 0.3431 0.4396 > N N 14.0067 0.227 A 0.3261 0.2889 > H1 H1 1.0079 0.200 A 0.2571 0.1842 > H2 H2 1.0079 0.200 A 0.2571 0.1842 > HA HA 1.0079 0.200 A 0.2571 0.1842 > HB1 HB1 1.0079 0.200 A 0.2571 0.1842 > HB2 HB2 1.0079 0.200 A 0.2571 0.1842 > HB3 HB3 1.0079 0.200 A 0.2571 0.1842 > H H 1.0079 0.200 A 0.2571 0.1842 > HA1 HA1 1.0079 0.200 A 0.2571 0.1842 > HA2 HA2 1.0079 0.200 A 0.2571 0.1842 > HG1 HG1 1.0079 0.200 A 0.2571 0.1842 > HG2 HG2 1.0079 0.200 A 0.2571 0.1842 > HD1 HD1 1.0079 0.200 A 0.2571 0.1842 > HD2 HD2 1.0079 0.200 A 0.2571 0.1842 > HE HE 1.0079 0.200 A 0.2571 0.1842 > HH21 HH21 1.0079 0.200 A 0.2571 0.1842 > HH22 HH22 1.0079 0.200 A 0.2571 0.1842 > HH11 HH11 1.0079 0.200 A 0.2571 0.1842 > HH12 HH12 1.0079 0.200 A 0.2571 0.1842 > HG HG 1.0079 0.200 A 0.2571 0.1842 > HD HD 1.0079 0.200 A 0.2571 0.1842 > HW1 HW1 1.0079 0.200 A 0.2571 0.1842 > HW2 HW2 1.0079 0.200 A 0.2571 0.1842 > O O 15.9994 -0.390 A 0.3118 0.2512 > > > > #include <ge.itp> > > ; Include Position restraint file > #ifdef POSRES > #include "posre-gel.itp" > #endif > > #include <peg.itp> > > ; Include Position restraint file > #ifdef POSRES > #include "posre-pe.itp" > #endif > > [ system ] > GEL and PE > > [ molecules ] > GEL 5 > PE 2 > > > > And now I am performing EM in vacuum for the system. The error comes to be > it stops Energy minimization before the desired energy is reached. > Like I read from other error mails, it says the topology or the itp file > had defects. > > > My query is, I just added charges to the itp file generated from OBGMX. > Is that the reason why my energy minimization is stopping at the middle. > > Kindly help with this. > > > Karpurmanjari > > > > > > > > > > > On Mon, Nov 5, 2018 at 10:46 PM Karpurmanjari Kakati < > ch18resch01...@iith.ac.in> wrote: > > > Dear Justin, > > > > I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the > > aminoacids.rtp file . I have all the files of OPLS AA force field in my > > working directory. > > For that I tried to generate the initial rtp format file from the hydroxy > > proline's .pdb and .gro files using the following command: > > gmx x2top -f hyd.gro -r hyd.rtp -pbc -ff oplsaa > > > > and I got the following error: > > > > Opening force field file > /usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t > > There are 23 name to type translations in file oplsaa.ff > > Generating bonds from distances... > > atom 18 > > Can not find forcefield for atom CA-2 with 4 bonds > > Can not find forcefield for atom C-3 with 3 bonds > > Can not find forcefield for atom CD-7 with 4 bonds > > > > ------------------------------------------------------- > > Program: gmx x2top, version 2018.1 > > Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 205) > > > > Fatal error: > > Could only find a forcefield type for 15 out of 18 atoms. > > > > > > Can you help me with this. > > > > I want to add this residue to the rtp file so that I can use the step > > pdb2gmx directly. > > > > > > Aijoni > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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