Re: [gmx-users] error in ATOM2CG.awk script

2009-08-28 Thread sunny mishra 
Yeah I agree wiht you but I tested another protein as well 1BL8 to check if
there was a problem specifically in 1K4C. Even after testing 1BL8 it gives
me the same error. What do you think?

On Thu, Aug 27, 2009 at 4:11 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Dear all,
>>
>> I was earlier facing problem regarding the mismatch of atoms in .top and
>> .gro file and then after useful discussion here I figured out that some
>> atoms were missing in my cg.pdb file and that problem is because of the
>> OLDER atom2cg.awk script which MARTINI folks have in their website. When I
>> was using the earlier version of atom2cg.awk script I had 776 atoms in my
>> .gro file and 804 atoms in .itp file and thats why .top and .gro were not
>> matching but again the same problem raised even after using the new
>> atom2cg.awk script which they sent me but it included some ILE residues and
>> now I have 784 atoms in .gro file and 804 atoms in .itp file
>>
>>
> As I recall, the root problem was that the original .pdb file from the RCSB
> had missing atoms that you had not properly modeled back in.
>
>  I pretty much now know how to fix the script but I am confused in some of
>> the things like:
>>
>> 1) In the cleaned.pdb file of my protein the ARG residue in the
>> atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2. If I
>> want to include other atoms as well like NH1, NH2, CZ, CD etc what should I
>> print for these atoms (either BN0, SC1, or SC2). As a matter of fact I don't
>> know what do SC1, BN0, SC2 mean?
>>
>
> Hence the point of CG.  You don't account for every single atom that was in
> the atomistic structure.  BN0 = backbone particle, SC1 and SC2 are side
> chain particles that will be given specific attributes in the topology.
>
> You should probably refer to the MARTINI publications for a more clear
> understanding of how the force field was conceived and how it should be
> used.
>
> -Justin
>
>  So, i don't know while adding other atoms for ARG residue what should I
>> print for them and I searched in the martini website but could not find
>> anything. Please let me know if you got my problem.
>>
>> Thanks,
>>
>> Sunny
>>
>>
>>
>> 
>>
>> ___
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>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
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> Please search the archive at http://www.gromacs.org/search before posting!
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>
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Re: [gmx-users] error in ATOM2CG.awk script

2009-08-28 Thread XAvier Periole 


On Aug 27, 2009, at 2:51 PM, sunny mishra wrote:


Dear all,

I was earlier facing problem regarding the mismatch of atoms in .top  
and .gro file and then after useful discussion here I figured out  
that some atoms were missing in my cg.pdb file and that problem is  
because of the OLDER atom2cg.awk script which MARTINI folks have in  
their website. When I was using the earlier version of atom2cg.awk  
script I had 776 atoms in my .gro file and 804 atoms in .itp file  
and thats why .top and .gro were not matching but again the same  
problem raised even after using the new atom2cg.awk script which  
they sent me but it included some ILE residues and now I have 784  
atoms in .gro file and 804 atoms in .itp file


I pretty much now know how to fix the script but I am confused in  
some of the things like:

Could you explain what was wrong and how you've fixed it.
Who gave you the new file?
1) In the cleaned.pdb file of my protein the ARG residue in the  
atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2.  
If I want to include other atoms as well like NH1, NH2, CZ, CD etc  
what should I print for these atoms (either BN0, SC1, or SC2). As a  
matter of fact I don't know what do SC1, BN0, SC2 mean?
I am not sure what you actually intent to do but adding atoms to use  
on the CG level does not sound

like something you'll want to do.
SC1/SC2 are the names for the side chains beads and BN0 is for the  
backbone bead with the

type N0.


So, i don't know while adding other atoms for ARG residue what  
should I print for them and I searched in the martini website but  
could not find anything. Please let me know if you got my problem.


Thanks,

Sunny


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Re: [gmx-users] error in ATOM2CG.awk script

2009-08-27 Thread Justin A. Lemkul 



sunny mishra wrote:
Yeah I agree wiht you but I tested another protein as well 1BL8 to check 
if there was a problem specifically in 1K4C. Even after testing 1BL8 it 
gives me the same error. What do you think?




1BL8 has a huge amount of atoms missing in the crystal structure, too.  Be aware 
of REMARK 470 lines in .pdb files that list missing atoms.


-Justin

On Thu, Aug 27, 2009 at 4:11 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

Dear all,

I was earlier facing problem regarding the mismatch of atoms in
.top and .gro file and then after useful discussion here I
figured out that some atoms were missing in my cg.pdb file and
that problem is because of the OLDER atom2cg.awk script which
MARTINI folks have in their website. When I was using the
earlier version of atom2cg.awk script I had 776 atoms in my .gro
file and 804 atoms in .itp file and thats why .top and .gro were
not matching but again the same problem raised even after using
the new atom2cg.awk script which they sent me but it included
some ILE residues and now I have 784 atoms in .gro file and 804
atoms in .itp file


As I recall, the root problem was that the original .pdb file from
the RCSB had missing atoms that you had not properly modeled back in.


I pretty much now know how to fix the script but I am confused
in some of the things like:

1) In the cleaned.pdb file of my protein the ARG residue in the
atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and
SC2. If I want to include other atoms as well like NH1, NH2, CZ,
CD etc what should I print for these atoms (either BN0, SC1, or
SC2). As a matter of fact I don't know what do SC1, BN0, SC2 mean?


Hence the point of CG.  You don't account for every single atom that
was in the atomistic structure.  BN0 = backbone particle, SC1 and
SC2 are side chain particles that will be given specific attributes
in the topology.

You should probably refer to the MARTINI publications for a more
clear understanding of how the force field was conceived and how it
should be used.

-Justin

So, i don't know while adding other atoms for ARG residue what
should I print for them and I searched in the martini website
but could not find anything. Please let me know if you got my
problem.

Thanks,

Sunny





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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] error in ATOM2CG.awk script

2009-08-27 Thread Justin A. Lemkul 



sunny mishra wrote:

Dear all,

I was earlier facing problem regarding the mismatch of atoms in .top and 
.gro file and then after useful discussion here I figured out that some 
atoms were missing in my cg.pdb file and that problem is because of the 
OLDER atom2cg.awk script which MARTINI folks have in their website. When 
I was using the earlier version of atom2cg.awk script I had 776 atoms in 
my .gro file and 804 atoms in .itp file and thats why .top and .gro were 
not matching but again the same problem raised even after using the new 
atom2cg.awk script which they sent me but it included some ILE residues 
and now I have 784 atoms in .gro file and 804 atoms in .itp file




As I recall, the root problem was that the original .pdb file from the RCSB had 
missing atoms that you had not properly modeled back in.


I pretty much now know how to fix the script but I am confused in some 
of the things like:


1) In the cleaned.pdb file of my protein the ARG residue in the 
atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2. If I 
want to include other atoms as well like NH1, NH2, CZ, CD etc what 
should I print for these atoms (either BN0, SC1, or SC2). As a matter of 
fact I don't know what do SC1, BN0, SC2 mean? 



Hence the point of CG.  You don't account for every single atom that was in the 
atomistic structure.  BN0 = backbone particle, SC1 and SC2 are side chain 
particles that will be given specific attributes in the topology.


You should probably refer to the MARTINI publications for a more clear 
understanding of how the force field was conceived and how it should be used.


-Justin

So, i don't know while adding other atoms for ARG residue what should I 
print for them and I searched in the martini website but could not find 
anything. Please let me know if you got my problem.


Thanks,

Sunny





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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] error in ATOM2CG.awk script

2009-08-27 Thread sunny mishra 
Dear all,
I was earlier facing problem regarding the mismatch of atoms in .top and
.gro file and then after useful discussion here I figured out that some
atoms were missing in my cg.pdb file and that problem is because of the
OLDER atom2cg.awk script which MARTINI folks have in their website. When I
was using the earlier version of atom2cg.awk script I had 776 atoms in my
.gro file and 804 atoms in .itp file and thats why .top and .gro were not
matching but again the same problem raised even after using the new
atom2cg.awk script which they sent me but it included some ILE residues and
now I have 784 atoms in .gro file and 804 atoms in .itp file

I pretty much now know how to fix the script but I am confused in some of
the things like:

1) In the cleaned.pdb file of my protein the ARG residue in the atom2cg.awk
script takes only CA, CG and NE with BN0, SC1, and SC2. If I want to include
other atoms as well like NH1, NH2, CZ, CD etc what should I print for these
atoms (either BN0, SC1, or SC2). As a matter of fact I don't know what do
SC1, BN0, SC2 mean?

So, i don't know while adding other atoms for ARG residue what should I
print for them and I searched in the martini website but could not find
anything. Please let me know if you got my problem.

Thanks,

Sunny
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