Hi Teri,
Can you send me the related files? I can try to debug the code.
Best,
Pengfei
2015-07-27 15:36 GMT-04:00 Eleftherios A P Lambros <tlambros.uci.edu>:
> Hello,
>
> I am getting a mismatch error on the 3rd step of MCPB.py as follows,
>
> Input script
> MCPB.py -i TS3.in -s 3b
>
> Output..
> The input file you are using is : TS3.in
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> The following is the input variable you have:
> The variable original_pdb is : WTDBD_TS3_CU_protonated.pdb
> The variable ion_ids is : [3011]
> The variable ion_mol2files is : ['CU.mol2']
> The variable group_name is : TS3
> The variable cut_off is : 2.8
> The variable chgfix_resids is : []
> The variable scmodel_chg is : -99
> -99 means program will assign a charge automatically.
> The variable lgmodel_chg is : -99
> -99 means program will assign a charge automatically.
> The variable software_version is : g09
> The variable sqm_opt is : 0
> The variable large_opt is : 0
> The variable force_field is : ff14SB
> The variable gaff is : 1
> The variable frcmodfs is : ['TS#.frcmod']
> The variable scale_factor is : 1.0
> Attention: The force constants will be scaled by
> multiplying the square of scale_factor.
> The variable bondfc_avg is : 0
> The variable anglefc_avg is : 0
> The variable naa_mol2files is : ['TS#.mol2']
> The variable software_version is : g09
> The variable water_model is : TIP3P
> The variable ion_paraset is : CM (Only for nonbonded model)
> The variable ion_info is : []
> ******************************************************************
> * *
> *======================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...
> =========================Checking models==========================
> ***Check the large model...
> Good. The charges and atom numbers are match for the large model.
> Good. There are 57 atoms in the large model.
> ***Check the standard model...
> Traceback (most recent call last):
> File "/mnt/net_share/home/tlambros/amber15-with-patches/bin/MCPB.py",
> line 581, in <module>
> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
> File
>
> "/mnt/net_share/home/tlambros/amber15-with-patches/lib/python2.7/site-packages/mcpb/resp_fitting.py",
> line 517, in resp_fitting
> raise pymsmtError('Error: the charges and atom numbers are mismatch '
> pymsmtexp.pymsmtError: Error: the charges and atom numbers are mismatch for
> the standard model!
>
> Looking at the most recent call we have,
>
> if len(stlist) != len(stdict):
> raise pymsmtError('Error: the charges and atom numbers are mismatch '
> 'for the standard model!')
>
> Where stlist and stdict are generated as follows,,,
>
>
> metcenres1 = [] #original name of the metal center residue
> stlist = [] #get the atom name list from the standard model
> stf = open(stfpf, 'r')
> for line in stf:
> if line[0:4] != "LINK":
> line = line.strip('\n')
> line = line.split()
> stlist.append(line[0])
> line = line[0].split('-')
> lresname = line[0] + '-' + line[1]
> if lresname not in metcenres1:
> metcenres1.append(lresname)
> stf.close()
>
> llist = [] #get the atom name list from the large model
> lf = open(lgfpf, 'r')
> for line in lf:
> line = line.strip('\n')
> llist.append(line)
> lf.close()
>
> ldict = {} #get charge of the large model, one-to-one relationship
> for i in range(0, len(llist)):
> ldict[llist[i]] = chgs[i]
>
> stdict = {} #get the charge of the standard model
> for i in ldict.keys():
> if i in stlist:
> stdict[i] = ldict[i]
>
>
> >From my understanding, MCPB.py will generate an atom and charge list from
> the large model from the large model pdb and resp files respectively. To
> generate the charge list for the standard model, it takes atoms from the
> standard model, and if there exists the same atom in the large model, it
> assigns that atom its corresponding charge from the large model charge
> list. That is, the standard model is a proper subset of the large model. I
> have checked to my standard model pdb and fingerprint files and they are
> not missing or have any extra atoms. (The tutorial files worked just fine
> for this step) I compared the format of the corresponding pdb and
> fingerprint files from the tutorial and found no difference in format (i.e.
> the standard models had complete residues etc...)
>
> The previous steps worked so I assume my gaussian 09 calculations went
> without any problems. Any help on this is appreciated.
>
> *NOTE* I am using the developmental release of pymsmt
>
> Thanks,
> Teri (Eleftherios) Lambros
> --
> Mathematics, School of Physical Sciences
> Biochemistry and Molecular Biology, School of Biological Sciences
> University of California: Irvine
>
> President, Anteaters Mathematics Club
> Advocacy Committee, Biological Sciences Student Council
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>
--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Tue Jul 28 2015 - 20:30:02 PDT
