GROMACS version:2019
GROMACS modification: No
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I would like to request you to suggest me to overcome the issue that I face during the energy minimization step in gromacs. I had a small peptide which I had immersed in DMSO and water molecules using Packmol.Now MDS is to be performed to this protein-water-DMSO box. As per the existing protocol the pdb2gmx cannot be performed for such boxes, so the topol.top file was generated manually. the command
gmx_mpi editconf -bt cubic -f protein.pdb -o protein-box.gro -c -d 1.0 was successful.
But the command gmx_mpi grompp -f minim.mdp -p topol.top -c protein-box.gro -o em.tpr -maxwarn 10 has shown the error. The DMSO.gro and .itp file were generated using the Acpype server. Plz suggest the needful.
Attached the images for your kind reference.
Thanks in advance
Regards
When you’re including new topologies, you need to make sure that all [atomtypes] are listed in the topology file before any [moleculetypes] are defined (see the manual for details). You’ll need to make sure this is the case in the topol.top. What you could try is moving all the atomtypes listed in the .itp file and list them explicitly in the topol.top file before any other the molecule types are defined, or alternatively moving any moleculetypes from the .itp file and listing them explicitly in the topol.top file after all the atomtypes are defined. The manual also has sections on topologies and topology files.
Also, I don’t advise using -maxwarn, it more often than not means ignoring mistakes that cause problems later during the simulation
Dear Dr. Karis,
Thank you for your quick response. I repeat, here my area of interest is a peptide solvated in DMSO and water using Packmol. This solvated box is further to be energy minimized followed by MDS. As per the existing protocol of gromacs we cannot use pdb2gmx, hence manually topol.top has to be performed. There is also no question of .itp file generation. Yes you are right if it would be a normal protein or protein-ligand complex. plz suggest me how to generate .itp in this packmol solvated box.
From my understanding of the problem, the error isn’t to do with anything specific to protein-ligand or packmol, it’s about the order in which the different sections of the topology files were called. Your topol.top should include the information from the forcefield and .itp files in an order such that no [moleculetype] is included before any [atomtype].
If your DMSO.itp file includes its own [atomtype] section followed by a [moleculetype] section, you need to make sure in the topol.top file that no [moleculetype] section is placed before the #include DMSO.itp command (whether it’s listed explicitly or in an #include command to another .itp file), and no [atomype] section is placed after, or you could take those sections from the .itp file and place them explicitly in the topol.top file to make sure this is true.
Is it possible for you to post the .itp file and .top file you’re using? It might help to see whether something is wrong with the files
Dear Karis,
Thanks for your response.I am here enclosing the files for your ready reference. The DMSO.gro and DMSO.itp files were generated through the ACpype server. The topolo.top was manually prepared.
I noticed you included the DMSO.itp file twice in the topol.top file:
; Include DMSO parameters #include “DMSO.itp”
; Include protein parameters #include “DMSO.itp”
Assuming the protein itself doesn’t need additional parameters not already present in the forcefield, does removing the second instance of #include “DMSO.itp” fix the issue?
If you did need to include a second .itp file for the protein, I would suggest copy-pasting the contents of the .itp files into the topol.top files explicity instead of relying on the #include commands, so you can make sure that all the [atomtypes] sections are defined before the [moleculetype] sections
Dear Karis,
Thanks for the response, but after removal of #include “DMSO.itp” , I have got a new Fatal error as "Number of coordinates in coordinate file (Protein.gro) does not match the Topology (Topol.top)
Now this time I have added ;Include water toplology, # include "oplsaa.ff/spc.itp, and in another line ;Include protein parameters, # include "oplsaa.ff/spc.itp,
after giving the command : gmx_mpi grompp -f minim.mdp -p topol.top -c protein.gro -o em.tpr
I had got a error1 [file spce.itp line3] Moleculetype SOL is redefined
Including spc.itp twice means including the parameters for your solvent twice, which is why the error is saying the moleculetype for SOL is redefined. Unless the protein requires an additional .itp file to be included, you can remove the ; Include protein parameters section.
Regarding the first error on the number of coordinates for the protein.gro, you also need the [ moleculetype ] defined for your protein. The most straightforward way would be to run pdb2gmx on just your protein file (since the forcefield should already contain the topologies defined for standard amino acids) to get the [ moleculetype ] section for the protein from the resulting topol.top, then copy-paste that section into your new topol.top file after the #include DMSO.itp command and make note of it under the [ molecules ] sections at the end. Let me know if that works!
Dear Karis,
Thanks for the response. I have tried pdb2gmx but could not get .itp file for my peptide. Actually it is a peptide with non-standard amino acid so I am unable to get the .itp. plz suggest the needful so that I could get the .itp file and hope your suggestions may work after getting .itp file.
Dear Karis,
I had successfully generated the .itp file for my peptide from ACPYPE server. Now I am having .itp for DMSO and my peptide. I have defined these in my topol.top But still I am getting the same error “Moleculetype UNK is redefined” . Can you plz share any protocol to solve such issues.
I don’t think there’s anything wrong with the overall method you’re doing, the issues seem to be in how you include the .itp files generated by acpype. That error suggests you’ve included the topology for UNK twice, similar to how you included DMSO.itp and spc.itp twice earlier in this thread. To clarify, are you keeping the information for both the DMSO and peptide in the same .itp file? If that is the case, you only need to #include .itp once in the topol.top file.
Also as mentioned before, make sure any [atomtype] sections from both are listed before any [moleculetype] sections. The program needs to have a list of all possible atomtypes before it starts grouping them into moleculetypes, otherwise it will return an error. So if you’re including the topologies from the .itp files of both DMSO and the protein in the same file, you need to move the [atomtype] sections for both the DMSO and protein to the top of the file before any of the [moleculetype] sections.
If this is still unclear, would you be able to share the input files you’re using by putting them in a google drive folder and sharing the link?
Dear Karis,
Thanks for your suggestions, I had prepared the files (packmol.pdb, topol.top,etc) accordingly. The commands shared by you and Aishwarya were successful in EM, but in the next NVT command: gmx_mpi mdrun -v -s nvt.tpr -o nvt.trr -e nvt.edr -c protein-nvt.gro -g nvt.log
it reflected a Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 67 atoms. The longest distance involved in such interactions is
4.688 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.
