normal g_sas

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6 years 2 weeks ago #1420 by is
g_sas was created by is
Hi,

I was using g_sas on CG structure. I changed accordingly probe radii to one corresponding to CG bead (0.235, although I found on this forum that it should be 0.265 (?)), however during calculations I got warning:

WARNING: could not find a Van der Waals radius for 876 atoms
145 out of 169 atoms were classified as hydrophobic

I searched for solution on the Gromacs mailing list and it appears that this warning is due to missing definition of radii for specific atom e.g. phosphor, that has to be defined in vdwradii.dat file. That is in the case of atomistic structures, but I assume the same is true when performing g_sas on CG structure. Therefore, I would like to know how to adjust vdwradii.dat file to match the CG description, or maybe someone already made this changes to vdwradii.dat and could share the file? Also, I suspect that depending on the used water model i.e. standard or polarizable I will have to remove or add charge sites, respectively, in vdwradii.dat, am I correct?

I'm using 4.5.3 version of Gromacs.

Thank you in advance
Iwona

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6 years 2 weeks ago #1421 by is
Replied by is on topic g_sas
I made preliminary vdwradii.dat file for CG system:

; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; '???' or '*' matches any residue name
; 'AAA' matches any protein residue name
;BB
??? BBc 0.235
??? BBh 0.235
??? BBs 0.235
??? BBt 0.235
;SC - ring
HIS S1c 0.215
HIS S2c 0.215
HIS S3c 0.215
HIS S1h 0.215
HIS S2h 0.215
HIS S3h 0.215
HIS S1s 0.215
HIS S2s 0.215
HIS S3s 0.215
HIS S1t 0.215
HIS S2t 0.215
HIS S3t 0.215
PHE S1c 0.215
PHE S2c 0.215
PHE S3c 0.215
PHE S1h 0.215
PHE S2h 0.215
PHE S3h 0.215
PHE S1s 0.215
PHE S2s 0.215
PHE S3s 0.215
PHE S1t 0.215
PHE S2t 0.215
PHE S3t 0.215
TRP S1c 0.215
TRP S2c 0.215
TRP S3c 0.215
TRP S4c 0.215
TRP S1h 0.215
TRP S2h 0.215
TRP S3h 0.215
TRP S4h 0.215
TRP S1s 0.215
TRP S2s 0.215
TRP S3s 0.215
TRP S4s 0.215
TRP S1t 0.215
TRP S2t 0.215
TRP S3t 0.215
TRP S4t 0.215
TYR S1c 0.215
TYR S2c 0.215
TYR S3c 0.215
TYR S1h 0.215
TYR S2h 0.215
TYR S3h 0.215
TYR S1s 0.215
TYR S2s 0.215
TYR S3s 0.215
TYR S1t 0.215
TYR S2t 0.215
TYR S3t 0.215
;SC - rest
ARG S1c 0.235
ARG S2c 0.235
ARG S1h 0.235
ARG S2h 0.235
ARG S1s 0.235
ARG S2s 0.235
ARG S1t 0.235
ARG S2t 0.235
ASN S1c 0.235
ASN S1h 0.235
ASN S1s 0.235
ASN S1t 0.235
ASP S1c 0.235
ASP S1h 0.235
ASP S1s 0.235
ASP S1t 0.235
CYS S1c 0.235
CYS S1h 0.235
CYS S1s 0.235
CYS S1t 0.235
GLN S1c 0.235
GLN S1h 0.235
GLN S1s 0.235
GLU S1c 0.235
GLU S1h 0.235
GLU S1s 0.235
GLU S1t 0.235
ILE S1c 0.235
ILE S1h 0.235
ILE S1s 0.235
ILE S1t 0.235
LEU S1c 0.235
LEU S1h 0.235
LEU S1s 0.235
LEU S1t 0.235
LYS S1c 0.235
LYS S2c 0.235
LYS S1h 0.235
LYS S2h 0.235
LYS S1s 0.235
LYS S2s 0.235
LYS S1t 0.235
LYS S2t 0.235
MET S1c 0.235
MET S1h 0.235
MET S1s 0.235
MET S1t 0.235
PRO S1c 0.235
PRO S1h 0.235
PRO S1s 0.235
PRO S1t 0.235
SER S1c 0.235
SER S1h 0.235
SER S1s 0.235
SER S1t 0.235
THR S1c 0.235
THR S1h 0.235
THR S1s 0.235
THR S1t 0.235
VAL S1c 0.235
VAL S1h 0.235
VAL S1s 0.235
VAL S1t 0.235
; Water charge sites - standard water model
W W 0.235
; Water charge sites - polarizable water model
PW WP 0
PW WM 0
PW W 0.235
;Ions
ION NA+ 0.235
ION CL- 0.235

although, I have some concerns. The charged particles in polarizable water model do not have vdw radii, correct? So when using -probe 0.235 these two charged particles radii will be overwritten with the applied probe radii. If I don't use the -probe option I will get the default value for probe radii (0.14). Therefore, my question is how to handle -probe when performing g_sas on a system with polarizable water model?

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6 years 1 week ago #1435 by xavier
Replied by xavier on topic g_sas
Hi Iwona,

First, does g_sas accepts your changes in the the file?
Second, why do you use the vdW radui of 0.235 nm and 0.215 nm? These seem to be half the epsilon value of the LJ potential, which is not the vdW radius but the value at which the LJ potential cross the zero energy value. The correct vdW radius (as given in many places) is 0.265 nm. It is the distance at the minimum of the LJ potential. You can easily find it by plotting any LJ potential of MARTINI.
The same goes for the probe. It must have the size of a MARTINI bead.

I hope this helps.

is wrote: I made preliminary vdwradii.dat file for CG system:

; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; '???' or '*' matches any residue name
; 'AAA' matches any protein residue name
;BB
??? BBc 0.235
??? BBh 0.235
??? BBs 0.235
??? BBt 0.235
;SC - ring
HIS S1c 0.215
HIS S2c 0.215
HIS S3c 0.215
HIS S1h 0.215
HIS S2h 0.215
HIS S3h 0.215
HIS S1s 0.215
HIS S2s 0.215
HIS S3s 0.215
HIS S1t 0.215
HIS S2t 0.215
HIS S3t 0.215
PHE S1c 0.215
PHE S2c 0.215
PHE S3c 0.215
PHE S1h 0.215
PHE S2h 0.215
PHE S3h 0.215
PHE S1s 0.215
PHE S2s 0.215
PHE S3s 0.215
PHE S1t 0.215
PHE S2t 0.215
PHE S3t 0.215
TRP S1c 0.215
TRP S2c 0.215
TRP S3c 0.215
TRP S4c 0.215
TRP S1h 0.215
TRP S2h 0.215
TRP S3h 0.215
TRP S4h 0.215
TRP S1s 0.215
TRP S2s 0.215
TRP S3s 0.215
TRP S4s 0.215
TRP S1t 0.215
TRP S2t 0.215
TRP S3t 0.215
TRP S4t 0.215
TYR S1c 0.215
TYR S2c 0.215
TYR S3c 0.215
TYR S1h 0.215
TYR S2h 0.215
TYR S3h 0.215
TYR S1s 0.215
TYR S2s 0.215
TYR S3s 0.215
TYR S1t 0.215
TYR S2t 0.215
TYR S3t 0.215
;SC - rest
ARG S1c 0.235
ARG S2c 0.235
ARG S1h 0.235
ARG S2h 0.235
ARG S1s 0.235
ARG S2s 0.235
ARG S1t 0.235
ARG S2t 0.235
ASN S1c 0.235
ASN S1h 0.235
ASN S1s 0.235
ASN S1t 0.235
ASP S1c 0.235
ASP S1h 0.235
ASP S1s 0.235
ASP S1t 0.235
CYS S1c 0.235
CYS S1h 0.235
CYS S1s 0.235
CYS S1t 0.235
GLN S1c 0.235
GLN S1h 0.235
GLN S1s 0.235
GLU S1c 0.235
GLU S1h 0.235
GLU S1s 0.235
GLU S1t 0.235
ILE S1c 0.235
ILE S1h 0.235
ILE S1s 0.235
ILE S1t 0.235
LEU S1c 0.235
LEU S1h 0.235
LEU S1s 0.235
LEU S1t 0.235
LYS S1c 0.235
LYS S2c 0.235
LYS S1h 0.235
LYS S2h 0.235
LYS S1s 0.235
LYS S2s 0.235
LYS S1t 0.235
LYS S2t 0.235
MET S1c 0.235
MET S1h 0.235
MET S1s 0.235
MET S1t 0.235
PRO S1c 0.235
PRO S1h 0.235
PRO S1s 0.235
PRO S1t 0.235
SER S1c 0.235
SER S1h 0.235
SER S1s 0.235
SER S1t 0.235
THR S1c 0.235
THR S1h 0.235
THR S1s 0.235
THR S1t 0.235
VAL S1c 0.235
VAL S1h 0.235
VAL S1s 0.235
VAL S1t 0.235
; Water charge sites - standard water model
W W 0.235
; Water charge sites - polarizable water model
PW WP 0
PW WM 0
PW W 0.235
;Ions
ION NA+ 0.235
ION CL- 0.235

although, I have some concerns. The charged particles in polarizable water model do not have vdw radii, correct? So when using -probe 0.235 these two charged particles radii will be overwritten with the applied probe radii. If I don't use the -probe option I will get the default value for probe radii (0.14). Therefore, my question is how to handle -probe when performing g_sas on a system with polarizable water model?

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6 years 1 week ago #1445 by is
Replied by is on topic g_sas
Hi Xavier,

Thank you for your answer.
First, yes g_sas accepts my changes to the file, and I don't get any more warnings like this:
WARNING: could not find a Van der Waals radius for 876 atoms
145 out of 169 atoms were classified as hydrophobic

Second, true the given values 0.235 and 0.215 are the half of the epsilon of the LJ potential for standard and ring beads, respectively. I will change the 0.235 nm to 0.265 nm. Is the 0.265 nm radii also true for the ring particles?

Yes, your answer helped, thank you, but still it does not solve my problem when using g_sas on the system with polarizable water model. I think I would have to make changes in the g_sas program, so that it will use the probe radii of 0.265 nm as a default value when not using the -probe option. Thus, maybe I will avoid overwriting the radii for the charged particles on polarizable water bead, am I right?

Best
Iwona

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6 years 1 week ago #1447 by xavier
Replied by xavier on topic g_sas

is wrote: Hi Xavier,

Thank you for your answer.
First, yes g_sas accepts my changes to the file, and I don't get any more warnings like this:
WARNING: could not find a Van der Waals radius for 876 atoms
145 out of 169 atoms were classified as hydrophobic

Second, true the given values 0.235 and 0.215 are the half of the epsilon of the LJ potential for standard and ring beads, respectively. I will change the 0.235 nm to 0.265 nm. Is the 0.265 nm radii also true for the ring particles?

Yes, your answer helped, thank you, but still it does not solve my problem when using g_sas on the system with polarizable water model. I think I would have to make changes in the g_sas program, so that it will use the probe radii of 0.265 nm as a default value when not using the -probe option. Thus, maybe I will avoid overwriting the radii for the charged particles on polarizable water bead, am I right?

Best
Iwona


Well ...

I am not sure of the value for the rings particles ... you can calculate it easily using standard expressions or plotting the potential.

For the polarizable water ... the charges do not carry vdW interactions so their radius should be zero. You could even remove them from the trajectory before treatment and consider they are regular water beads.

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6 years 1 week ago #1449 by is
Replied by is on topic g_sas

xavier wrote:
Well ...

I am not sure of the value for the rings particles ... you can calculate it easily using standard expressions or plotting the potential.


I calculated vdW radii for ring beads to be 0.24 nm.

xavier wrote: For the polarizable water ... the charges do not carry vdW interactions so their radius should be zero. You could even remove them from the trajectory before treatment and consider they are regular water beads.


I did that.
Thank you for your help.

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6 years 1 week ago #1456 by xavier
Replied by xavier on topic g_sas
Tks, now we have the official size of ring particle :)) 0.24 nm


is wrote:

xavier wrote:
Well ...

I am not sure of the value for the rings particles ... you can calculate it easily using standard expressions or plotting the potential.


I calculated vdW radii for ring beads to be 0.24 nm.

xavier wrote: For the polarizable water ... the charges do not carry vdW interactions so their radius should be zero. You could even remove them from the trajectory before treatment and consider they are regular water beads.


I did that.
Thank you for your help.

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