- Posts: 210
Periodic dimerization and backward.py mapping
- Robin
-
Topic Author
- Visitor
7 years 3 months ago #6919
by Robin
Periodic dimerization and backward.py mapping was created by Robin
Hello everyone,
I am currently studying dimerization interface of 2 proteins in martini representation, and trying to backmap the system (dimer+membrane) in order to study it in all atom later.
My first problem concern directly one of my dimers which dimerized at the extremity of the box. I am pretty sure the dimerization happened since I can see the dimer by using periodic images. But evidently, when I try to locate interacting residue (this script is pretty usefull for that purpose: www.ks.uiuc.edu/Research/vmd/mailing_lis...5681/newcontacts.tcl ), the script doesn't see the interacting image.
I tried several combination of gmx trjconv to make one of the protomer the center:
gmx trjconv -f half101prot10ns.trr -s dimer.gro -o recentered10ns.trr -b 0 -n mudelta.ndx -center -pbc whole -boxcenter
But no success, my protomers stay at the opposite periodic "wall".
My second problem concern backward.py handling of the POPC lipid:
want: H91
have:
Bailing out...
I know this problem has already been adressed :
So I changed the POPC mapping using this page: cgmartini.nl/index.php/force-field-param...ml?dir=PC&lipid=POPC .
The error is still the same despite using the 2.0 martini rule. Do you have any other idea of what could cause this problem?
Thank you for reading :).
Robin
I am currently studying dimerization interface of 2 proteins in martini representation, and trying to backmap the system (dimer+membrane) in order to study it in all atom later.
My first problem concern directly one of my dimers which dimerized at the extremity of the box. I am pretty sure the dimerization happened since I can see the dimer by using periodic images. But evidently, when I try to locate interacting residue (this script is pretty usefull for that purpose: www.ks.uiuc.edu/Research/vmd/mailing_lis...5681/newcontacts.tcl ), the script doesn't see the interacting image.
I tried several combination of gmx trjconv to make one of the protomer the center:
gmx trjconv -f half101prot10ns.trr -s dimer.gro -o recentered10ns.trr -b 0 -n mudelta.ndx -center -pbc whole -boxcenter
But no success, my protomers stay at the opposite periodic "wall".
My second problem concern backward.py handling of the POPC lipid:
want: H91
have:
Bailing out...
I know this problem has already been adressed :
flaviyan wrote: Hi Chris,
You are using the Martini lipid rule 2.0 for the POPC [12 beads] (which is the case in the latest insane script) but you are using the Mapping scheme according to the old lipid rules [13 beads]. so the backward is throwing an error. Either update the Mapping to match the new bead description or use the following insane command:
./insane.py -o cg.gro -p cg.top -l POPC.o:1 -x 10 -y 10 -z 10
So I changed the POPC mapping using this page: cgmartini.nl/index.php/force-field-param...ml?dir=PC&lipid=POPC .
The error is still the same despite using the 2.0 martini rule. Do you have any other idea of what could cause this problem?
Thank you for reading :).
Robin
Please Log in or Create an account to join the conversation.
- peterkroon
-
- Offline
- Gold Boarder
Less
More
7 years 3 months ago #6925
by peterkroon
Replied by peterkroon on topic Periodic dimerization and backward.py mapping
To give you a solution for your first problem (hopefully): try centering on a residue (preferrably one at the interface) rather than on the dimer as a whole.
Please Log in or Create an account to join the conversation.
- Robin
-
Topic Author
- Visitor
7 years 3 months ago - 7 years 3 months ago #6930
by Robin
Replied by Robin on topic Periodic dimerization and backward.py mapping
Thank you for your advice :). I tried centering on one monomer, interface residu from both monomers (4 in each) and I still got monomers contacting at PBC limits. Maybe I need multiple trjconv calls.
Finally, It seems the following command did the trick (much more simple than I though):
gmx trjconv -f halfsystem201.trr -s prod1.tpr -pbc cluster -o halfprot102.trr
My dimer is finally whole!
Still no solution for backward.py.
Finally, It seems the following command did the trick (much more simple than I though):
gmx trjconv -f halfsystem201.trr -s prod1.tpr -pbc cluster -o halfprot102.trr
My dimer is finally whole!
Still no solution for backward.py.
Last edit: 7 years 3 months ago by Robin. Reason: actualisation
Please Log in or Create an account to join the conversation.
- Robin
-
Topic Author
- Visitor
7 years 3 months ago - 7 years 3 months ago #6964
by Robin
Replied by Robin on topic Periodic dimerization and backward.py mapping
Ok so I managed to pass through the H91 problem (seems like It was still searching in the old topology even with the name change). The next problem I got come from the trans operation it seems:
[('H45', None), ('C47', None), ('C1', (1.0376332995838211, 5.433177095506531, 4.253398502591266)), ('O2', None)]
Not all positions defined for [trans] operation:
[('H46', None), ('C47', None), ('C1', (1.0376332995838211, 5.433177095506531, 4.253398502591266)), ('O2', None)]
Not all positions defined for [trans] operation:
[('C44', None), ('C47', None), ('C1', (1.594848688419134, 8.273678175555368, 4.4328742475019665)), ('O2', None)]
I think this problem is linked to the POPC mapping but I don't understand really how it works.
Anyway, It doesn't seem to be a critical error since it continue to minimization until this error arise:
Fatal error:
Atomtype SP1 not found
I know it seems to be a ELnedyn atom (representation i'm using) but in my martini file used for backmapping, trp only got the BB, SC1, SC2, SC3 and SC4 types. Of course, this atome doesn't appear in the 0-backward.gro file either. Does it means that gmx or backward are expecting the SP1 atometype that doesn't exist in my files?
Update: it seems backward.py doesn't FG the cholesterol residue in my file. Pretty strange since it does for POPC and all the residue of my protein: the .map file of chol is in the same folder as the others.
[('H45', None), ('C47', None), ('C1', (1.0376332995838211, 5.433177095506531, 4.253398502591266)), ('O2', None)]
Not all positions defined for [trans] operation:
[('H46', None), ('C47', None), ('C1', (1.0376332995838211, 5.433177095506531, 4.253398502591266)), ('O2', None)]
Not all positions defined for [trans] operation:
[('C44', None), ('C47', None), ('C1', (1.594848688419134, 8.273678175555368, 4.4328742475019665)), ('O2', None)]
I think this problem is linked to the POPC mapping but I don't understand really how it works.
Anyway, It doesn't seem to be a critical error since it continue to minimization until this error arise:
Fatal error:
Atomtype SP1 not found
I know it seems to be a ELnedyn atom (representation i'm using) but in my martini file used for backmapping, trp only got the BB, SC1, SC2, SC3 and SC4 types. Of course, this atome doesn't appear in the 0-backward.gro file either. Does it means that gmx or backward are expecting the SP1 atometype that doesn't exist in my files?
Update: it seems backward.py doesn't FG the cholesterol residue in my file. Pretty strange since it does for POPC and all the residue of my protein: the .map file of chol is in the same folder as the others.
Last edit: 7 years 3 months ago by Robin.
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
7 years 3 months ago #6978
by tsjerk
Replied by tsjerk on topic Periodic dimerization and backward.py mapping
It almost looks like you use a coarse grained target topology. The atomtype error is what Gromacs says during minimization, indicating that the topology mentions an SP1 type particle. Can you assert that you provide a coarse grained structure file and an atomistic target topology?
Please Log in or Create an account to join the conversation.
- Robin
-
Topic Author
- Visitor
7 years 3 months ago - 7 years 2 months ago #6990
by Robin
Replied by Robin on topic Periodic dimerization and backward.py mapping
You are right, I did forgot to change the chol.itp since I got the other all atoms topology files from the aquaporine backmapping tutorial. Thank you very much for your help! Do you know where I could find itp topology file for charmm36?
I tried to make an chol.itp file from one standard cholesterol in all-atom, and from the charmm 36 forcefield. Problem is the name and atom numbering doesn't seem to be the same in chol.charmm36.map and the charmm36 forcefield. Does anyone know from what all atom topology the cholesterol mapping was done? Only solution I see for my problem is replacing one by one the name of the 74 cholesterol atoms in the map file.
Moreover I think I spotted an error in the chol.charmm36.map:
[out]
C52 C50 C56 C24
H53 C50 C56 C24
H54 C50 C56 C24
H44 C50 C56 C24
The H44 atom doesn't exist in the [ atom ] section, I guess H44=C44?
I tried to make an chol.itp file from one standard cholesterol in all-atom, and from the charmm 36 forcefield. Problem is the name and atom numbering doesn't seem to be the same in chol.charmm36.map and the charmm36 forcefield. Does anyone know from what all atom topology the cholesterol mapping was done? Only solution I see for my problem is replacing one by one the name of the 74 cholesterol atoms in the map file.
Moreover I think I spotted an error in the chol.charmm36.map:
[out]
C52 C50 C56 C24
H53 C50 C56 C24
H54 C50 C56 C24
H44 C50 C56 C24
The H44 atom doesn't exist in the [ atom ] section, I guess H44=C44?
Last edit: 7 years 2 months ago by Robin.
Please Log in or Create an account to join the conversation.
Time to create page: 0.099 seconds