Re: [AMBER] Query regarding the workflow

From: Abhi Acharya <>
Date: Wed, 16 Nov 2016 16:15:23 +0530

Hello Amber users,

Perhaps my question was not clear previously.

I have been trying to calculate charges for active site metal ions and the
coordinating residues using the seminario method. i follow the tutorial by
Pengfei et al.

These are the steps I followed:

1. created the pdb for the protein model with Hydrogens added. Also created
the mol2 files for active site water molecules (single file with 4
molecules) and ions (one each for Cu and Ca ion).
2. Next I proceeded to generate the small and large active site models
using GAMESS.
3. Performed geometry optimization and fc calculation for small model.
Optimized the large model and performed charge calculations using GAMESS.
4. Generated the frcmod file for the active site using the command: -i -s 2

So far so good. My problem is the following:
A. How to proceed after creating the initial frcmod file i.e after the
second step -i input -s 2. Everything works smoothly till this
step. However, in the next step: -i input -s 3

I get the following error:
The following is the input variable you have:
The variable ion_ids is : [3825, 3826]
The variable ion_info is : []
The variable ion_mol2files is : ['CA.mol2', 'CU.mol2']
The variable original_pdb is : 3UJO_fixed_H.pdb
The variable add_bonded_pairs is : []
The variable additional_resids is : []
The variable anglefc_avg is : 0
The variable bondfc_avg is : 0
The variable cut_off is : 2.8
The variable chgfix_resids is : []
The variable force_field is : ff14SB
The variable frcmodfs is : []
The variable gaff is : 1
The variable group_name is : 3UJO
The variable ion_paraset is : CM (Only for nonbonded model)
The variable large_opt is : 1
The variable lgmodel_chg is : -99
             -99 means program will assign a charge automatically.
The variable naa_mol2files is : ['WAT.mol2']
The variable scale_factor is : 1.0
             ATTENTION: This is the scale factor of frequency. The
             force constants will be scaled by multiplying the square
             of scale_factor.
The variable smmodel_chg is : -99
             -99 means program will assign a charge automatically.
The variable software_version is : gms
The variable sqm_opt is : 0
The variable water_model is : TIP3P
* *
*======================RESP Charge fitting=======================*
* *
***Generating the 1st stage resp charge fitting input file...
***Generating the 2nd stage resp charge fitting input file...
***Doing the RESP charge fiting...
Traceback (most recent call last):
  File "/home/bp-lab/install-fold/amber16/bin/", line 600, in
    premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
line 443, in resp_fitting
    get_esp_from_gms(mklogf, espf)
line 222, in get_esp_from_gms
    for i in range(bln, eln+1):
UnboundLocalError: local variable 'eln' referenced before assignment

B. I did not find any mol2 files generated for the active site coordinating
residues. Perhaps, these files will be generated if the above errors are
Am I correct?

Kindly help.

Thanks and Regards,
Abhishek Acharya

On Sat, Nov 12, 2016 at 2:39 PM, Abhi Acharya <>

> Hi amber users,
> I am trying to use the workflow to derive parameters for an active
> site containing Cu2+ and Ca2+ ions. The Cu2+ ion is coordinated by two
> water molecules, and active site residues Asp, His etc.
> My question is that in the input file for do we need to specify
> separate mol2 files for the two water molecules and the coordinating
> residues? In the tutorial at this link:
> the input
> file does not specify any of the coordinating His residues. But still in
> the 3rd step i.e. -i -s 3, the tutorial says that mol2
> files for HD1, HD2 and HE1 will be created. I am a bit confused.
> I request you to kindly clarify this.
> Thanks and Regards,
> Abhishek Acharya
> CFTRI, Mysore.
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Received on Wed Nov 16 2016 - 03:00:02 PST
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