CG mapping of molecule with symmetrical topology

[Roozbeh R]

Dear All,

I intend to prepare a cg topology file for a peptide fragment which is a symmetrical molecule i.e. there is two copies of each residue in the atomistic model of my molecule albeit with different segment id in the pdb file. I wish to map the atomistic model to a cg model in which each of the symmetrical parts is mapped into a separate cg bead. i wonder how can i  make votca consider each of these redundant residues as part of a separate CG bead, because in the mapping section of the example topology files of votca tutorials, each atom mapped to the cg bead is designated  by  a "resid: resname :atomname" combination which in my case would point to 2 different atoms (each with a different segment id in the atomistic model ,e.g. PROA vs PROB) so  actually this it is not sufficient to point to the one specific atom, instead it will point to 2 atoms which leaves me wondering  how (and if) votca can understand which atom belongs  to which bead in this case? will it choose between the 2 atoms randomly ? or is there a method to further articulate atom/cg bead association?

thank you for the valuable support,

Roozi  

[Christoph Junghans]

On Sun, Feb 18, 2024 at 11:47 PM Roozbeh R <rooz...@gmail.com> wrote:
>
> Dear All,
> I intend to prepare a cg topology file for a peptide fragment which is a symmetrical molecule i.e. there is two copies of each residue in the atomistic model of my molecule albeit with different segment id in the pdb file. I wish to map the atomistic model to a cg model in which each of the symmetrical parts is mapped into a separate cg bead. i wonder how can i make votca consider each of these redundant residues as part of a separate CG bead, because in the mapping section of the example topology files of votca tutorials, each atom mapped to the cg bead is designated by a "resid: resname :atomname" combination which in my case would point to 2 different atoms (each with a different segment id in the atomistic model ,e.g. PROA vs PROB) so actually this it is not sufficient to point to the one specific atom, instead it will point to 2 atoms which leaves me wondering how (and if) votca can understand which atom belongs to which bead in this case? will it choose between the 2 atoms randomly ? or is there a method to further articulate atom/cg bead association?

VOTCA (and GROMACS) use some form of "resid:resname:atomname" as an
identifier, if that is not unique for your case, you will have to
change your topology, so it can be mapped by csg_map. Or write the
topology file by hand without mapping.

Christoph

>
> thank you for the valuable support,
> Roozi
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Roozbeh R]

Hi Christoph,

Thank you for the reply. Ok, I see. 

One more question arises regarding Topology file of atomistic model: my protein pdb file (and hence topology file) starts from resid 392 (as its been extracted from a bigger protein fragment) . when i run  csg_map, an error message appear regarding the first atom mapped to the CG bead :  molecule 392:GLY:N does not exist . when i check AA topology input of votca, via csg_dump --top topol.tpr, however i can see that the first atom identifier is: 0 Name 1:GLY:N Type NH3 Mass 14.007 Resnr 0 Resname GLY Charge -0.3 , which means votca disregards the resid as listed in the original topology file, in which the first resid is 392, and reset/initiate res ids from 1. this is quite problematic for a case like mine as all topology/coordinate files are automatically generated base on data banks info / XRD files. 

so i wonder is there a workaround to make votca consider residues resids as written in the topology file and not reset them to start from 1?

kind regards,

[Christoph Junghans]

On Tue, Feb 20, 2024 at 4:17 PM Roozbeh R <rooz...@gmail.com> wrote:
>
> Hi Christoph,
> Thank you for the reply. Ok, I see.
> One more question arises regarding Topology file of atomistic model: my protein pdb file (and hence topology file) starts from resid 392 (as its been extracted from a bigger protein fragment) . when i run csg_map, an error message appear regarding the first atom mapped to the CG bead : molecule 392:GLY:N does not exist . when i check AA topology input of votca, via csg_dump --top topol.tpr, however i can see that the first atom identifier is: 0 Name 1:GLY:N Type NH3 Mass 14.007 Resnr 0 Resname GLY Charge -0.3 , which means votca disregards the resid as listed in the original topology file, in which the first resid is 392, and reset/initiate res ids from 1. this is quite problematic for a case like mine as all topology/coordinate files are automatically generated base on data banks info / XRD files.
> so i wonder is there a workaround to make votca consider residues resids as written in the topology file and not reset them to start from 1?

Nope, no workaround, but you should be able to hack VOTCA's source to
do what you want pretty easily.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/3e6086b3-627f-4401-ac23-937d871acfe9n%40googlegroups.com.

[Roozbeh R]

Well am not very efficient in coding ,but i think it is worth giving it a shot .  so would you please point to where shall i begin for this specific case of resid initiation? i already checked votca source and found : "~\votca\csg\src\tools\csg_map.cc" . Is this the file to be modified? and if so, shall i modify some other CC files/headers/etc. too?
 kindly please advise,

[Christoph Junghans]

On Tue, Feb 20, 2024 at 3:49 PM Roozbeh R <rooz...@gmail.com> wrote:
>
> Well am not very efficient in coding ,but i think it is worth giving it a shot . so would you please point to where shall i begin for this specific case of resid initiation? i already checked votca source and found : "~\votca\csg\src\tools\csg_map.cc" . Is this the file to be modified? and if so, shall i modify some other CC files/headers/etc. too?

I think you have two options: modify the mapper in
csg/src/libcsg/map.cc or modify the writer in
csg/src/libcsg/modules/io/pdbwriter.cc.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/5996666c-d658-4f1e-9bd6-d135b2dc1f44n%40googlegroups.com.

[Roozbeh R]

Hi,

I have also a question regarding order of atoms listing in cg bead definition in the mapping file. Is it safe to say that it is NOT a mandatory requirement by votca to list the atomistic beads which are mapped to a cg bead in the topology section of the mapping file in a weight-descending order? obviously it seems votca prefers that to be the case based on examples and tutorials & actually i tested it already in hexane tutorial , via flipping the order in which a carbon and a hydrogen atoms are listed in mapping of one of the beads (naturally did the same to the weights) and it seems it is not causing any problems for converting AA to CG. Still i would rather reconfirm it here now than notice sth is wrong later. and  if my thinking is right, is this descending listing some sort of a speed booster for faster mapping of atomistic trajectory into a cg one?  

thank you for the clarification.

roozi

[Christoph Junghans]

On Sun, Feb 25, 2024, 21:14 Roozbeh R <rooz...@gmail.com> wrote:

Hi,

I have also a question regarding order of atoms listing in cg bead definition in the mapping file. Is it safe to say that it is NOT a mandatory requirement by votca to list the atomistic beads which are mapped to a cg bead in the topology section of the mapping file in a weight-descending order? obviously it seems votca prefers that to be the case based on examples and tutorials & actually i tested it already in hexane tutorial , via flipping the order in which a carbon and a hydrogen atoms are listed in mapping of one of the beads (naturally did the same to the weights) and it seems it is not causing any problems for converting AA to CG. Still i would rather reconfirm it here now than notice sth is wrong later. and  if my thinking is right, is this descending listing some sort of a speed booster for faster mapping of atomistic trajectory into a cg one?  

The order doesn't matter! Also no speed loss.

Christoph

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/e33eb821-5faa-4abe-93f2-daf9ef22dc45n%40googlegroups.com.