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reverse transformatiom
- satyan
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14 years 3 days ago #356
by satyan
reverse transformatiom was created by satyan
Hi,
I am trying to do CG to FG transformation, using the g_fg2cg tool.
In my cg.top I have
Protein 1
POPC 128
W 1499
NA+ 1
and in my fg.top I have
Protein 1
POPC 128
FG_W 5996 ;1499*4
NA+ 1
The command
g_fg2cg -pfg fg.top -pcg cg.top -n 0 -c hlwi_SA2.gro -o out_fg.gro
goes fine but in out_fg.gro, I find that all waters after 1657 (which happens to be 1500th water) have been assigned 0.000 coordinates as shown here
1657FG_W OW24939 1.196 3.087 4.785
1657FG_W HW124940 1.131 3.184 4.701
1657FG_W HW224941 1.295 3.157 4.713
1658FG_W OW24942 0.000 0.000 0.000
1658FG_W HW124943 0.000 0.000 0.000
1658FG_W HW224944 0.000 0.000 0.000
1658FG_W OW24945 0.000 0.000 0.000
1658FG_W HW124946 0.000 0.000 0.000
1658FG_W HW224947 0.000 0.000 0.000
.
.
.
6153FG_W HW178892 0.000 0.000 0.000
6153FG_W HW278893 0.000 0.000 0.000
6154NA+ NA78894 0.000 0.000 0.000
6.62085 6.62085 8.28885
Using this out_fg.gro leads to segmentation fault in mdrun. If I delete all these waters (1658-6153) and modify the out_fg.gro and fg.top files, mdrun runs smoothly.
I dont know why is it so.
regards,
satyan
I am trying to do CG to FG transformation, using the g_fg2cg tool.
In my cg.top I have
Protein 1
POPC 128
W 1499
NA+ 1
and in my fg.top I have
Protein 1
POPC 128
FG_W 5996 ;1499*4
NA+ 1
The command
g_fg2cg -pfg fg.top -pcg cg.top -n 0 -c hlwi_SA2.gro -o out_fg.gro
goes fine but in out_fg.gro, I find that all waters after 1657 (which happens to be 1500th water) have been assigned 0.000 coordinates as shown here
1657FG_W OW24939 1.196 3.087 4.785
1657FG_W HW124940 1.131 3.184 4.701
1657FG_W HW224941 1.295 3.157 4.713
1658FG_W OW24942 0.000 0.000 0.000
1658FG_W HW124943 0.000 0.000 0.000
1658FG_W HW224944 0.000 0.000 0.000
1658FG_W OW24945 0.000 0.000 0.000
1658FG_W HW124946 0.000 0.000 0.000
1658FG_W HW224947 0.000 0.000 0.000
.
.
.
6153FG_W HW178892 0.000 0.000 0.000
6153FG_W HW278893 0.000 0.000 0.000
6154NA+ NA78894 0.000 0.000 0.000
6.62085 6.62085 8.28885
Using this out_fg.gro leads to segmentation fault in mdrun. If I delete all these waters (1658-6153) and modify the out_fg.gro and fg.top files, mdrun runs smoothly.
I dont know why is it so.
regards,
satyan
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- andrzej
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14 years 3 days ago #357
by andrzej
Replied by andrzej on topic reverse transformatiom
Hey
You got FG_W 5996 and W 1499. When You check FG_W itp file ( it is in tutorial files as far as i remember ), one FG_W molecule is actually for spc like waters, 12 atoms, so FG_W and W numbers should be equal
A
You got FG_W 5996 and W 1499. When You check FG_W itp file ( it is in tutorial files as far as i remember ), one FG_W molecule is actually for spc like waters, 12 atoms, so FG_W and W numbers should be equal
A
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- satyan
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14 years 3 days ago #358
by satyan
Replied by satyan on topic reverse transformatiom
hello,
So, I have 4 spc's both in CG and FG_W and thats why there no. shouldnot be changed. OK, now when I in my fg.top to I have FG_W 1499 (same as W in cg.top), I get
processing topology...
Generated 5 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein 1
Excluding 1 bonded neighbours for POPC 128
Excluding 1 bonded neighbours for W 1499
Excluding 1 bonded neighbours for NA+ 1
Number of fg atoms 24930
Number of cg atoms 3227
Reading frames from gro file 'PROT IN POPC BILAYER', 3227 atoms.
Reading frame 0 time 0.000 1271414242
Name of CG water in topology should be W
Segmentation fault
then if I use FG_W 1500, i get
processing topology...
Generated 5 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein 1
Excluding 1 bonded neighbours for POPC 128
Excluding 1 bonded neighbours for W 1499
Excluding 1 bonded neighbours for NA+ 1
Number of fg atoms 24942
Number of cg atoms 3227
Reading frames from gro file 'PROT IN POPC BILAYER', 3227 atoms.
Reading frame 0 time 0.000 1271414146
Name of CG water in topology should be W
Fg pre-structure computed !
but the out_fg.gro has
1657FG_W OW24939 1.307 3.136 4.682
1657FG_W HW124940 1.341 3.123 4.590
1657FG_W HW224941 1.063 3.123 4.773
1658NA+ NA24942 0.000 0.000 0.000
6.62085 6.62085 8.28885
Still not very clear to me.
regards,
satyan
So, I have 4 spc's both in CG and FG_W and thats why there no. shouldnot be changed. OK, now when I in my fg.top to I have FG_W 1499 (same as W in cg.top), I get
processing topology...
Generated 5 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein 1
Excluding 1 bonded neighbours for POPC 128
Excluding 1 bonded neighbours for W 1499
Excluding 1 bonded neighbours for NA+ 1
Number of fg atoms 24930
Number of cg atoms 3227
Reading frames from gro file 'PROT IN POPC BILAYER', 3227 atoms.
Reading frame 0 time 0.000 1271414242
Name of CG water in topology should be W
Segmentation fault
then if I use FG_W 1500, i get
processing topology...
Generated 5 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein 1
Excluding 1 bonded neighbours for POPC 128
Excluding 1 bonded neighbours for W 1499
Excluding 1 bonded neighbours for NA+ 1
Number of fg atoms 24942
Number of cg atoms 3227
Reading frames from gro file 'PROT IN POPC BILAYER', 3227 atoms.
Reading frame 0 time 0.000 1271414146
Name of CG water in topology should be W
Fg pre-structure computed !
but the out_fg.gro has
1657FG_W OW24939 1.307 3.136 4.682
1657FG_W HW124940 1.341 3.123 4.590
1657FG_W HW224941 1.063 3.123 4.773
1658NA+ NA24942 0.000 0.000 0.000
6.62085 6.62085 8.28885
Still not very clear to me.
regards,
satyan
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- satyan
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14 years 3 days ago #359
by satyan
Replied by satyan on topic reverse transformatiom
Hello,
So problem was solved by moving NA+ just after POPC and before W in cg.gro.
But its still strange that g_fg2cg doesnot care for atleast one more additional number of FG_W in fg.top as compared to W in cg.top.
regards,
satyan
So problem was solved by moving NA+ just after POPC and before W in cg.gro.
But its still strange that g_fg2cg doesnot care for atleast one more additional number of FG_W in fg.top as compared to W in cg.top.
regards,
satyan
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- andrzej
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14 years 3 days ago #360
by andrzej
Replied by andrzej on topic reverse transformatiom
Do You have mapping section in Your ion itp file ? How did You construct that ? I never played with ions so You have to decide yourself how You map back atomistic details and test it, as far as i remember ion in Martini is defined as ion + some water molecules, check publications. Just to be sure: you constructed mapping section with modified pdb2gmx for protein and its in your itp file , and mappings for lipids are also defined in itp files , wright ?
Andrzej
Andrzej
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