There are no element symbols in columns 77 and 78 for your complex.pdb file.
They are present in the SSS.pdb file.
When viewing SSS.pdb with Discovery Studio 4.5 the chlorine atom is
recognized as such and is clearly visible. Complex.pdb contains no chlorine
atoms in Discovery Studio 4.5. VMD has similar problems.
Put the atomic symbols in columns 77 and 78 to fix your problem. When I do
that for CL1 it registers as a chlorine. If Tleap is stripping out the
atomic symbols, you need to find a way to stop it from doing that.
Jim
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Thursday, February 02, 2017 7:56 PM
To: 'AMBER Mailing List' <amber.ambermd.org>; jimkress_58.kressworks.org
Subject: Re: [AMBER] Tleap is making C instaed of Cl
See this is my pdb complex file in which ligand SSS is bound and it is
having element CL but still not of the visualizing software is predicting it
Cl, all software says it is C.
_____
From: Thakur, Abhishek
Sent: Thursday, February 2, 2017 1:45:00 PM
To: 'AMBER Mailing List'; jimkress_58.kressworks.org
<mailto:jimkress_58.kressworks.org>
Subject: Re: [AMBER] Tleap is making C instaed of Cl
Hi
I have crossed checked each and every line again, but CL element seems to be
present there.
_____
From: James Kress <jimkress_58.kressworks.org
<mailto:jimkress_58.kressworks.org> >
Sent: Thursday, February 2, 2017 1:00:19 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] Tleap is making C instaed of Cl
The tutorial pdb file you indicated HAS the elements in columns 77 and 78.
Your pdb file does not have the element CL in columns 77 and 78. That makes
the format of the pdb invalid.
Put the elements in columns 77 and 78 (2 character elements start in 77. 1
character elements start in 78) and try again.
Jim Kress
-----Original Message-----
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Thursday, February 02, 2017 5:24 PM
To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org> >;
david.case.rutgers.edu <mailto:david.case.rutgers.edu>
Subject: Re: [AMBER] Tleap is making C instaed of Cl
Hi,
Just now I have found an example file on amber tutorial which has used
tleap to make parameters for ligand containing Cl ions
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_ba
sic_tutorial4b_
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_b
asic_tutorial4b_&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&
m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6V
bAfHFm_TIBs6e2s&e=>
&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_GXQmdqWf7
a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6VbAfHFm_TIBs6e2s&
e=
I am using same structure and trying to reproduce and see if I get C or Cl,
I can observe similar trend, Cl being replaced by C.
As there is difference in frcmod file generated by both of us.
Frcmod file of tutorial is
remark goes here
MASS
BOND
ANGLE
ca-c3-c1 64.784 110.735 Calculated with empirical approach
c1-c1-cx 56.400 177.990 same as c1-c1-c3
c1-cx-hc 48.300 109.750 same as c1-c3-hc
c1-cx-cx 64.200 111.590 same as c1-c3-c3
DIHE
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
n -o -c -os 10.5 180.0 2.0 General improper
torsional angle (2 general atom types)
c -ca-n -hn 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
ca-ca-ca-n 1.1 180.0 2.0 Using default
value
Where as in my case I can see only
remark goes here
MASS
BOND
ANGLE
c1-c1-cx 56.280 178.460 same as c1-c1-c3
c1-cx-hc 48.250 109.750 same as c1-c3-hc
DIHE
IMPROPER
c -ca-n -hn 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
ca-ca-ca-n 1.1 180.0 2.0 Using default
value
ca-ca-ca-ha 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
n -o -c -os 10.5 180.0 2.0 General improper
torsional angle (2 general atom types)
NONBON
It seems tleap is not generating Cl parameters for me.
As I am following same procedure.
If there any parameter file that I need to download for Cl?
________________________________
From: Thakur, Abhishek
Sent: Thursday, February 2, 2017 11:22:23 AM
To: AMBER Mailing List; david.case.rutgers.edu
<mailto:david.case.rutgers.edu>
Subject: Re: [AMBER] Tleap is making C instaed of Cl
Hi,
Just now I have found an example file on amber tutorial which has used
tleap to make parameters for ligand containing Cl ions
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_ba
sic_tutorial4b_
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_b
asic_tutorial4b_&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&
m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6V
bAfHFm_TIBs6e2s&e=>
&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_GXQmdqWf7
a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6VbAfHFm_TIBs6e2s&
e=
I am using same structure and trying to reproduce and see if I get C or Cl,
I can observe similar trend, Cl being replaced by C.
As there is difference in frcmod file generated by both of us.
Frcmod file of tutorial is
remark goes here
MASS
BOND
ANGLE
ca-c3-c1 64.784 110.735 Calculated with empirical approach
c1-c1-cx 56.400 177.990 same as c1-c1-c3
c1-cx-hc 48.300 109.750 same as c1-c3-hc
c1-cx-cx 64.200 111.590 same as c1-c3-c3
DIHE
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
n -o -c -os 10.5 180.0 2.0 General improper
torsional angle (2 general atom types)
c -ca-n -hn 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
ca-ca-ca-n 1.1 180.0 2.0 Using default
value
Where as in my case I can see only
________________________________
From: Thakur, Abhishek
Sent: Thursday, February 2, 2017 10:56:50 AM
To: AMBER Mailing List; david.case.rutgers.edu
<mailto:david.case.rutgers.edu>
Subject: Re: [AMBER] Tleap is making C instaed of Cl
Hi
I have downloaded my receptor from RCSB website and have docked my ligand
with autodock.
The have build complex pdb with MGLTools.
Then I have use antechamber to calculate BCC charges.
Then I have used parmchk to generated frcmod file and tleap to generate
other files for ligand.
The taking library file and frcmod file of ligand with the tleap I have
build complex parmtop and inpcrd file and saved solvated complex pdb.
In this file I can see that at last position there is Cl, but chimera does
not change gree, neither maestro 2D visualizer shows it to be Cl.
It seems to be C, but still in pdb file there it has been outputted as Cl1.
ATOM 8320 Cl1 RRR 515 -7.533 -4.212 4.655 1.00 0.00
________________________________
From: David Case <david.case.rutgers.edu <mailto:david.case.rutgers.edu> >
Sent: Thursday, February 2, 2017 9:51:31 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Tleap is making C instaed of Cl
On Thu, Feb 02, 2017, Thakur, Abhishek wrote:
>
> As when I have input pdb file it had CL1 denotation for Chlorine atoms
> and in library file it has given me output as Cl1.
I too am confused: are you talking about the Atom name (in columns 13-16)
or the element (in columns 77-78)?
I don't think that you have told use exactly how you converted the "input
pdb file" into a "library file".
Second, when you refer to the "input pdb file", input to what? Is this what
you are inputting to tleap, or the file you are inputting to Chimera?
Just to repeat what I asked earlier:
>
> Look at the PDB file **you are actually loading in Chimera**: does the
> chlorine atom have the correct element (**columns 77-78 in the ATOM
> line**)? If not, we would need details about how you made the PDB
> file. If it looks OK, it might be a Chimera issue (although that sounds
kind of unlikely).
....dac
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Received on Thu Feb 02 2017 - 19:30:02 PST
