Hi, After running the dock prep, I get the following warning in the reply log. Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log How can I fix this warning? Do I need to fix this? Thank you for any help you can provide. I truly appreciate it. Chris
Hi Chris, This is generally due to missing atoms in those residues. If they had truncated side chains, there is an option in dock prep to fix that. If they are missing backbone atoms, however, you'd have to add them some other way. However, these are not huge deviations of charge so if they aren't near some binding site or area that you really care that much about, the effect wouldn't be that large and you could choose to disregard. Occasionally it will be due to unrecognized atom names, especially if you had hydrogens to start with, so you could also try removing all the original hydrogens and adding them back with dock prep. However, the missing atoms situation is much more likely. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2023, at 10:33 AM, Chris Ellis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
After running the dock prep, I get the following warning in the reply log.
Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log
How can I fix this warning? Do I need to fix this?
Thank you for any help you can provide. I truly appreciate it.
Chris
Thank you Elaine, this is very helpful. All the best, Chris On Thu, Aug 17, 2023 at 2:00 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Chris, This is generally due to missing atoms in those residues. If they had truncated side chains, there is an option in dock prep to fix that. If they are missing backbone atoms, however, you'd have to add them some other way. However, these are not huge deviations of charge so if they aren't near some binding site or area that you really care that much about, the effect wouldn't be that large and you could choose to disregard.
Occasionally it will be due to unrecognized atom names, especially if you had hydrogens to start with, so you could also try removing all the original hydrogens and adding them back with dock prep. However, the missing atoms situation is much more likely.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2023, at 10:33 AM, Chris Ellis via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi,
After running the dock prep, I get the following warning in the reply log.
Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log
How can I fix this warning? Do I need to fix this?
Thank you for any help you can provide. I truly appreciate it.
Chris
Hi Elaine, I fixed the problem amino acids but when I saved my charged mol2 file I get this error. *Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni)* *Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni)* What is the best way to fix this? Do I need to fix this? :) Thanks, Chris On Thu, Aug 17, 2023 at 2:00 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Chris, This is generally due to missing atoms in those residues. If they had truncated side chains, there is an option in dock prep to fix that. If they are missing backbone atoms, however, you'd have to add them some other way. However, these are not huge deviations of charge so if they aren't near some binding site or area that you really care that much about, the effect wouldn't be that large and you could choose to disregard.
Occasionally it will be due to unrecognized atom names, especially if you had hydrogens to start with, so you could also try removing all the original hydrogens and adding them back with dock prep. However, the missing atoms situation is much more likely.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2023, at 10:33 AM, Chris Ellis via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi,
After running the dock prep, I get the following warning in the reply log.
Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log
How can I fix this warning? Do I need to fix this?
Thank you for any help you can provide. I truly appreciate it.
Chris
Hi Chris, It is more of a warning than an error: simply that your file has atoms named NI which are interpreted as nickel (element symbol Ni) which does not have a SYBYL atom type. SYBYL atom type is part of the Mol2 output format. You can't do anything to fix it assuming that you want those nickel atoms. Chimera will do the best it can when writing SYBYL Mol2 format, which is simply to put the atom type as Ni in that output file. You'd need to investigate whether whatever program is actually going to use the Mol2 file will be able to interpret/use that or not. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2023, at 2:54 PM, Chris Ellis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I fixed the problem amino acids but when I saved my charged mol2 file I get this error.
Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni) Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni)
What is the best way to fix this? Do I need to fix this? :)
Thanks, Chris
On Thu, Aug 17, 2023 at 2:00 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Chris, This is generally due to missing atoms in those residues. If they had truncated side chains, there is an option in dock prep to fix that. If they are missing backbone atoms, however, you'd have to add them some other way. However, these are not huge deviations of charge so if they aren't near some binding site or area that you really care that much about, the effect wouldn't be that large and you could choose to disregard.
Occasionally it will be due to unrecognized atom names, especially if you had hydrogens to start with, so you could also try removing all the original hydrogens and adding them back with dock prep. However, the missing atoms situation is much more likely.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2023, at 10:33 AM, Chris Ellis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
After running the dock prep, I get the following warning in the reply log.
Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log
How can I fix this warning? Do I need to fix this?
Thank you for any help you can provide. I truly appreciate it.
Chris
Hi Elaine, Thank you so much again. I did come across another error when preparing the ligand. I went to tools -> structure editing -> add charge. It prompts me to add hydrogen bonds and estimates the ligand charge correctly. I then get this error... Failure running ANTECHAMBER for residue TP7 Check reply log for details Any ideas what I did wrong here? :) Thanks again Elaine, Chris [image: image.png] On Fri, Aug 18, 2023 at 6:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Chris, It is more of a warning than an error: simply that your file has atoms named NI which are interpreted as nickel (element symbol Ni) which does not have a SYBYL atom type. SYBYL atom type is part of the Mol2 output format. You can't do anything to fix it assuming that you want those nickel atoms. Chimera will do the best it can when writing SYBYL Mol2 format, which is simply to put the atom type as Ni in that output file. You'd need to investigate whether whatever program is actually going to use the Mol2 file will be able to interpret/use that or not. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2023, at 2:54 PM, Chris Ellis via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I fixed the problem amino acids but when I saved my charged mol2 file I get this error.
Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni) Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni)
What is the best way to fix this? Do I need to fix this? :)
Thanks, Chris
On Thu, Aug 17, 2023 at 2:00 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Chris, This is generally due to missing atoms in those residues. If they had truncated side chains, there is an option in dock prep to fix that. If they are missing backbone atoms, however, you'd have to add them some other way. However, these are not huge deviations of charge so if they aren't near some binding site or area that you really care that much about, the effect wouldn't be that large and you could choose to disregard.
Occasionally it will be due to unrecognized atom names, especially if you had hydrogens to start with, so you could also try removing all the original hydrogens and adding them back with dock prep. However, the missing atoms situation is much more likely.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2023, at 10:33 AM, Chris Ellis via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi,
After running the dock prep, I get the following warning in the reply log.
Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log
How can I fix this warning? Do I need to fix this?
Thank you for any help you can provide. I truly appreciate it.
Chris
Hi Chris, If the hydrogens and the charge estimate look right to you, you may not be doing anything wrong. Sometimes Antechamber AM1-BCC charge calculation just fails, especially on compounds with highly charged groups like phosphate. You may have to try using the simpler Gasteiger charge calculation method instead. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 21, 2023, at 6:28 AM, Chris Ellis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you so much again. I did come across another error when preparing the ligand. I went to tools -> structure editing -> add charge.
It prompts me to add hydrogen bonds and estimates the ligand charge correctly. I then get this error...
Failure running ANTECHAMBER for residue TP7 Check reply log for details
Any ideas what I did wrong here? :)
Thanks again Elaine, Chris
<image.png>
On Fri, Aug 18, 2023 at 6:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Chris, It is more of a warning than an error: simply that your file has atoms named NI which are interpreted as nickel (element symbol Ni) which does not have a SYBYL atom type. SYBYL atom type is part of the Mol2 output format. You can't do anything to fix it assuming that you want those nickel atoms. Chimera will do the best it can when writing SYBYL Mol2 format, which is simply to put the atom type as Ni in that output file. You'd need to investigate whether whatever program is actually going to use the Mol2 file will be able to interpret/use that or not. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2023, at 2:54 PM, Chris Ellis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I fixed the problem amino acids but when I saved my charged mol2 file I get this error.
Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni) Atom whose IDATM type has no equivalent Sybyl type: #0:1550.A@NI (type: Ni)
What is the best way to fix this? Do I need to fix this? :)
Thanks, Chris
On Thu, Aug 17, 2023 at 2:00 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Chris, This is generally due to missing atoms in those residues. If they had truncated side chains, there is an option in dock prep to fix that. If they are missing backbone atoms, however, you'd have to add them some other way. However, these are not huge deviations of charge so if they aren't near some binding site or area that you really care that much about, the effect wouldn't be that large and you could choose to disregard.
Occasionally it will be due to unrecognized atom names, especially if you had hydrogens to start with, so you could also try removing all the original hydrogens and adding them back with dock prep. However, the missing atoms situation is much more likely.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2023, at 10:33 AM, Chris Ellis via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
After running the dock prep, I get the following warning in the reply log.
Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log
How can I fix this warning? Do I need to fix this?
Thank you for any help you can provide. I truly appreciate it.
Chris
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