Hi there

The way that I usually define polymers in gromcas is using the residue based generation of the whole chain. in the aminoacid.rtp file in the opls-aa force field you can (you need a local copy of that. don't change the original one) add a residue for each specific type of monomer you have. Then you can generate the whole chain (and all of its bond, angle and torsions ) using pdb2gmx code (if you have the .pdb file). Editing a structure file you have (either .pdb or .* ) is required as pdb2gmx is so serious about the spacing in the text file. If you had more information I could help more.

Dear Abolfazl,

Thank you for your reply,

i was able to make the .top file after modifying the .rtp file. (aminoacid.rtp from line 1649)

i did it as follows..

[ atoms ]

C1 opls_240 0 1

C2 opls_145 -0.115 1

C3 opls_240 0 1

C4 opls_240 0 1

C5 opls_136 -0.12 1

C6 opls_136 -0.12 1

C7 opls_136 -0.12 1

C8 opls_136 -0.12 1

C9 opls_136 -0.12 1

C10 opls_136 -0.12 1

C11 opls_239 0 1

C12 opls_239 0 1

C13 opls_240 0 1

C14 opls_136 -0.12 1 and so on for 208 atoms.

and

[ bonds ]

C1 C2

C1 C13

C1 C82

C2 C3

C2 H28

C3 C4

C3 C5

C4 C11

C4 C21

C5 C6

C5 H29

C5 H30

C6 C7

C6 H31

C6 H32

C7 C8

C7 H33

C7 H34

C8 C9

for all the bonds. then i used

pdb2gmx -f polymer.pdb -o topol.gro -water spce

and it gave me topol1 .top file and topol.gro. but when i .top file was generating i got error messages as follow

Warning: Long Bond (1-2 = 0.712913 nm)

Warning: Long Bond (1-13 = 0.404954 nm)

Warning: Long Bond (1-82 = 0.271054 nm)

Warning: Long Bond (2-3 = 0.838742 nm)

Warning: Long Bond (2-28 = 0.672423 nm)

Warning: Long Bond (3-4 = 0.764106 nm)

Warning: Long Bond (3-5 = 0.314719 nm)

Warning: Long Bond (4-11 = 0.559873 nm)

i used that .top file and .gro with grompp here i got the fatal error

ERROR 253 [file topol.top, line 1940]:

No default Ryckaert-Bell. types

ERROR 254 [file topol.top, line 1941]:

No default Ryckaert-Bell. types

ERROR 255 [file topol.top, line 1942]:

No default Ryckaert-Bell. types

ERROR 256 [file topol.top, line 1943]:

No default Ryckaert-Bell. types

Excluding 3 bonded neighbours molecule type 'Other'

turning all bonds into constraints...

ERROR 257 [file topol.top, line 1969]:

ERROR: The cut-off length is longer than half the shortest box vector or

longer than the smallest box diagonal element. Increase the box size or

decrease rlist.

here i went through the topol1.top and gave the corresponding atom numbers to the di headrals where it generate the errors ( topl1.top line 1420 and so on)

to avoid the error 257 i used editconf and made another .gro file with larger dimensions( ffgro.gro)

after that when i use

grompp -f npt.mdp -c ffgro.gro -p topol1.top -o run.tpr

i still get a fatal error as follow.

There were 119 warnings

-------------------------------------------------------

Program grompp, VERSION 4.5.5

Source code file: grompp.c, line: 1372

Fatal error:

There were 137 errors in input file(s)

i am attaching all the files here with. please give me some suggestions.

Thank you!

Sidath

Hi Sidath.

You will have to manually edit the residue numbers of each polymer unit to not have the "long bond" issue.

If your polymer has no hydrogen initially, it is all good. If it has, you can use open babel to remove the hydrogens. Then make sure the name of Carbon/Oxygen/Nitrogen atoms that you have mentioned in your polymer exactly match the ones in .rtp. pdb2gmx will add hydrogens automatically. For the hydrogens to be added correctly, you will also have to edit the .hdb files. (Read the gromacs manual on the .hdb files, it is pretty easy to edit it).

Also, have the OPLS ff in your current directory and make changes in it and not the original one.

The command shoud be like:

pdb2gmx -ff oplsaa -f abc.pdb -o abc.gro

topol.top and posre.itp will be created. If you don't want the position restraints, comment out or delete its section created in the end part of the topology file.

Note: g_x2top is not a very reliable tool.

Hope this helps! :)