From: Thakur, Abhishek <>
Date: Mon, 26 Mar 2018 16:39:25 +0000

Hi Pengfei,

Thank you for your response. I have checked all those points in the system but still, it is giving the same error.

Will you mind looking into my system once?

I am sorry for disturbing you, but I have tried everything and still, it seems to give me a problem.

I will really appreciate your help.

Thanking you,


From: Pengfei Li <>
Sent: Monday, March 26, 2018 5:24:03 AM
To: AMBER Mailing List
Subject: Re: [AMBER]

Hi Abhishek,

It is an atom name error. Please check the following section in the tutorial: <>.

“ now supports more than 80 metal ions (see Figure 3 in the reference paper <>). For all of these metal ions and halide ions (if in the ion format but not neutral format), capitalized element name are suggested to use for both the residue name and atom name. Please make sure the residue name and atom name of the metal ion (not only for zinc used here) are all captilized (e.g. herein all equals "ZN", not "Zn", "zN", or "zn"), only in this way will recognize it as a metal ion. Meanwhile, please make sure each metal ion or halide ion (if it is in its ion format but not neutral format) is treated seperately as an indepedent residue in the PDB file. If you have metal site which has metal ion embeded in the ligand residue, for example, the HEME group in PDB file, please seperate the metal ion into an independent residue (also, with an unique residue number and atom number)in the PDB file. Meanwhile, in order to make recognize the atoms well, if you have atoms have atom names capitalized with numbers in your original PDB file (applies for protein or ligand), please change these atom names to atom names capitalized with their element symbols (for example, change "2HA1" to "HA12", change "1HAA" to "HAA1") in the PDB file before performing following steps.”

Hope it helps,

> On Mar 22, 2018, at 2:12 PM, Thakur, Abhishek <> wrote:
> Hi, I am having a small problem in generating gaussian input file using
> Kindly help me in solving this problem.
> The error that I am getting is.
> ***Creating the small model...
> It contains the residue 530-HID as sidechain coordinated.
> It contains the residue 534-HID as sidechain coordinated.
> It contains the residue 593-GLU as sidechain coordinated.
> It contains the residue 696-ZN as normal.
> It contains the residue 697-MOL as normal.
> It contains the residue 698-HOH as normal.
> Totally there are 83 atoms in the small model.
> Traceback (most recent call last):
> File "/nethome/axt651/apps/amber16_tools/bin/", line 644, in <module>
> addred, lgchg, lgspin)
> File "/nethome/axt651/apps/amber16_tools/lib/python2.7/site-packages/pymsmt/mcpb/", line 1895, in gene_model_files
> smspin, addred, outf, sqmopt)
> File "/nethome/axt651/apps/amber16_tools/lib/python2.7/site-packages/pymsmt/mcpb/", line 1380, in build_small_model
> AtNum = Atnum[gatm.element]
> KeyError: '1'
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Received on Mon Mar 26 2018 - 10:00:06 PDT
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