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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Received on Mon Jul 27 2015 - 13:00:03 PDT
