Thank you so much Daniel.
It works fine.
Is this a kind of bug in Tleap that for Cl it first reads C and ignores L?
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, February 3, 2017 2:47:29 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Tleap is making C instaed of Cl
You could run the pdb through cpptraj with the corresponding topology to
get the element symbols back.
parm complex.parm7
trajin complex.pdb
trajout complex.elements.pdb
Hope this helps,
-Dan
On Thu, Feb 2, 2017 at 10:14 PM James Kress <jimkress_58.kressworks.org>
wrote:
> 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_basic_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=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_basic_tutorial4b_&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6VbAfHFm_TIBs6e2s&e=>
> >
> &d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_
> GXQmdqWf7
> a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6VbA
> fHFm_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_basic_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=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_basic_tutorial4b_&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6VbAfHFm_TIBs6e2s&e=>
> >
> &d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_
> GXQmdqWf7
> a2utCarssvNk3DEwBNkiJGRoYPGuc&s=DldC3JL0XL36uTPdX1YnKSMQ2p6VbA
> fHFm_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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> ambermd.org_mailma
> n_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&
> m=MTp1Zbp1FRuioMLK9AJKDbgZzMHbky4k9PSZuVb4A3U&s=
> cfi48J7iHnf7uCY9OEMm--xWvgPm
> JV-OAm7NAmHGlDQ&e=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=MTp1Zbp1FRuioMLK9AJKDbgZzMHbky4k9PSZuVb4A3U&s=cfi48J7iHnf7uCY9OEMm--xWvgPmJV-OAm7NAmHGlDQ&e=>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> ambermd.org_mailma
> n_listinfo_amber
> <https://urldefense.proofpoint.com/v2/url?u=http-> 3A__lists.ambermd.org_mailm
> an_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg
> &m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=Qq5NneDBz93JeAra_
> KcIda0gAsP
> o00BgKTR2cZL-E1Y&e=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=Qq5NneDBz93JeAra_KcIda0gAsPo00BgKTR2cZL-E1Y&e=>
> >
> &d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_
> GXQmdqWf7
> a2utCarssvNk3DEwBNkiJGRoYPGuc&s=Qq5NneDBz93JeAra_
> KcIda0gAsPo00BgKTR2cZL-E1Y&
> e=
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> ambermd.org_mailma
> n_listinfo_amber
> <https://urldefense.proofpoint.com/v2/url?u=http-> 3A__lists.ambermd.org_mailm
> an_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg
> &m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=Qq5NneDBz93JeAra_
> KcIda0gAsP
> o00BgKTR2cZL-E1Y&e=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_GXQmdqWf7a2utCarssvNk3DEwBNkiJGRoYPGuc&s=Qq5NneDBz93JeAra_KcIda0gAsPo00BgKTR2cZL-E1Y&e=>
> >
> &d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=IttY_
> GXQmdqWf7
> a2utCarssvNk3DEwBNkiJGRoYPGuc&s=Qq5NneDBz93JeAra_
> KcIda0gAsPo00BgKTR2cZL-E1Y&
> e=
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=GNYgTQIQYhz4iYXH34ak-M6xoYb8OhrjOrHNx2i6yJ8&s=kikYk902ndTTbfzDmBl3z_Txb-DmXxOzdAt_uqgyQgo&e=
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=GNYgTQIQYhz4iYXH34ak-M6xoYb8OhrjOrHNx2i6yJ8&s=kikYk902ndTTbfzDmBl3z_Txb-DmXxOzdAt_uqgyQgo&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 03 2017 - 07:00:02 PST
