Hi Prasanth,
Glad it works. In my experience reduce can also add hydrogen atoms to ligand (but the atom IDs needs to be resequenced by other program such as pdb4amber), but maybe your case is different from mine.
Pengfei
> On Jan 27, 2019, at 6:06 AM, Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in> wrote:
>
> Hello Pengfei,
>
> I overcame the issue by following these steps using chimera:
> 1) Deleted all Hydrogens from HEM and ligand and save the resulting
> structures as HEM_h.pdb and LIG_h.pdb (specified to save in amber format
> and not hybrid...)
> 2) Reduce HEM_h.pdb using "reduce" command as suggested in the tutorial and
> save it as HEM_H.pdb
> 3) Added hydrogens to LIG_h.pdb using CHIMERA (used option AddH from
> structure editing) and saved it as LIG_H.pdb (specified to save in amber
> format and not hybrid...)
> 4) Perform other steps as suggested in tutorial and perform
> $ MCPB.py -i 3ln1.in -s 1
> and obtained the files for gaussian.
>
> I realized that amber would reduce only molecules that are recognized to be
> part of proteins/DNA. Also that it is important to rename the atoms in
> amber format. The problem occurred because the HEM of the original pdb file
> contained a few atoms with "1H.." as pointed out by Pengfei in his message.
>
> Thank you for the support.
> Regards,
> Prasanth.
>
> --------------------------------------
> In response to Pengfei's suggestion:
> Hi Prasanth,
>
> The correction you did for the FE.mol2 file is right. According to the the
> message you provided, I guess it is because the atom name problem in your
> PDB file, in which you have an atom name with ?1? as the first letter.
>
> The following contents from the webpage
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm> <
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>> could be
> helpful:
>
> Generally we need a PDB file of the protein, which should employ the format
> of PDB version 3.0? <
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html>>and
> be consistent with the AMBER naming scheme for residues (e.g. HID, HIE, HIP
> for HIS). We also need to prepare mol2 files for non-standard residues
> (such as the metal ion, water and ligand).
>
> Meanwhile, in order to make MCPB.py 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.
>
> After solving these potential issues, please regenerated the corresponding
> mol2 files which are relevant to this issue. And try ?MCPB.py -i 3ln1.in -s
> 1? again, to see whether it works.
>
> Hope it helps,
> Pengfei
>
> On Tue, Jan 22, 2019 at 12:17 PM Prasanth G, Research Scholar <
> prasanthghanta.sssihl.edu.in <mailto:prasanthghanta.sssihl.edu.in>> wrote:
>
>> Dear all,
>>
>> I am trying to work on a heme containing protein (COX-2) pdb id: 3ln1
>> docked with a few ligands (that are not in the vicinity of HEME group).
>>
>> I am trying to emulate the following tutorial to obtain the parameters for
>> the heme.
>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
>>
>> However, I am getting stuck because of an error at the first step of
>> MCPB.py
>> This is the command and the error:
>> ----------------------------------
>> $ MCPB.py -i 3ln1.in -s 1
>> ******************************************************************
>> * Welcome to use the MCPB.py program *
>> * Version 3.0 *
>> * Author: Pengfei Li *
>> * Merz Research Group *
>> * Michigan State University *
>> * AND *
>> * Hammes-Schiffer Research Group *
>> * University of Illinois at Urbana-Champaign *
>> ******************************************************************
>> The input file you are using is : 3ln1.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> The following is the input variable you have:
>> The variable ion_ids is : [8935]
>> The variable ion_info is : []
>> The variable ion_mol2files is : ['FE.mol2']
>> The variable original_pdb is : 3ln1_H_renum.pdb
>> The variable add_bonded_pairs is : []
>> The variable add_redcrd is : 0
>> The variable additional_resids is : []
>> The variable anglefc_avg is : 0
>> The variable bondfc_avg is : 0
>> The variable chgfix_resids is : []
>> The variable cut_off is : 2.8
>> The variable force_field is : ff14SB
>> The variable frcmod_files is : ['HEM.frcmod']
>> The variable gaff is : 1
>> The variable group_name is : 3ln1
>> The variable ion_paraset is : CM (Only for nonbonded model)
>> The variable large_opt is : 0
>> The variable lgmodel_chg is : -99
>> The variable lgmodel_spin is : -99
>> -99 means program will assign a charge automatically.
>> The variable naa_mol2files is : ['HEM.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
>> The variable smmodel_spin 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
>> The variable xstru is : 0
>> ******************************************************************
>> * *
>> *=======================Metal Site Information===================*
>> * *
>> ******************************************************************
>> ***Selected Metal ion FE is atom 8935 in residue 554-FE
>> 357-HIE.NE2 is in 2.8 Angstrom of or set bonded (in the input file) to
>> (one of) these metal ions
>> 553-HEM.NA is in 2.8 Angstrom of or set bonded (in the input file) to
>> (one of) these metal ions
>> 553-HEM.NB is in 2.8 Angstrom of or set bonded (in the input file) to
>> (one of) these metal ions
>> 553-HEM.NC is in 2.8 Angstrom of or set bonded (in the input file) to
>> (one of) these metal ions
>> 553-HEM.ND is in 2.8 Angstrom of or set bonded (in the input file) to
>> (one of) these metal ions
>> ***The following residues are in the Metal Site:
>> Residue 357-HIE
>> Residue 553-HEM
>> Residue 554-FE
>> ***The small model contains the following residues:
>> [357, 553, 554]
>> ***The large model contains the following residues:
>> [356, 357, 358, 553, 554]
>> ******************************************************************
>> * *
>> *=======================Building models==========================*
>> * *
>> ******************************************************************
>> ***Creating the small model...
>> It contains the residue 357-HIE as sidechain coordinated.
>> It contains the residue 553-HEM as normal.
>> It contains the residue 554-FE as normal.
>> Totally there are 88 atoms in the small model.
>> Traceback (most recent call last):
>> File "/home/cosmos10/amber16/bin/MCPB.py", line 644, in <module>
>> addred, lgchg, lgspin)
>> File
>> "/home/cosmos10/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
>> line 1895, in gene_model_files
>> smspin, addred, outf, sqmopt)
>> File
>> "/home/cosmos10/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
>> line 1380, in build_small_model
>> AtNum = Atnum[gatm.element]
>> KeyError: '1'
>> ------------------------------------------
>>
>> The 3ln1.in file is as follows:
>> original_pdb 3ln1_H_renum.pdb
>> group_name 3ln1
>> cut_off 2.8
>> ion_ids 8935
>> software_version gms
>> ion_mol2files FE.mol2
>> naa_mol2files HEM.mol2
>> frcmod_files HEM.frcmod
>> ----------------------------------------
>> Something strange that i observed in the FE.mol2
>> 1 FE 28.2000 -36.2200 -3.2730 f 605 FE 0.000000
>> I modified "f" to "FE" while changing the charge to 3.00000
>>
>> FE.mol2 is as follows:
>> .<TRIPOS>MOLECULE
>> FE
>> 1 0 1 0 0
>> SMALL
>> No Charge or Current Charge
>>
>>
>> .<TRIPOS>ATOM
>> 1 FE 28.2000 -36.2200 -3.2730 FE 605 FE
>> 3.000000
>> .<TRIPOS>BOND
>> .<TRIPOS>SUBSTRUCTURE
>> 1 FE 1 TEMP 0 **** **** 0 ROOT
>> ---------------------------
>>
>>
>> Can you kindly suggest, what needs to be done to fix this error.
>>
>> Thank you.
>>
>> --
>> Regards,
>> Prasanth.
>>
>
>
> --
> Regards,
> Prasanth.
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Received on Tue Feb 05 2019 - 08:30:03 PST
