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-- Shahid. On Tue, Jul 4, 2017 at 1:05 PM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote: > Dear Amber users, > > I am trying to parameterize Zn coordinated to HID, HID, GLU and a water > molecule and have been following the AMBER advanced tutorial 20 on MCPB.py. > > The sidechain model geometry was optimized, force constants calculated for > the large model and the sidechain model fchk file generated. > Next, the Merz-Kollman RESP charge calculation was done followed by the > Gaussian 09 bug fix and espgen in AMBER. > > The tutorial mentions that you should confirm that coordination bonds do > not break. How do I check for this? > > In the final modelling step using the gaussian output I get the following > error: > > [llubbe.login2 04072017_MCPBpycontd]$ MCPB.py -i 03072017_NDOM.in -s 2 > > > > ****************************************************************** > * Welcome to use MCPB.py program * > * Author: Pengfei Li * > * Merz Research Group * > * Michigan State University * > * All Rights Reserved * > ****************************************************************** > > > > The input file you are using is : 03072017_NDOM.in > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > The following is the input variable you have: > The variable original_pdb is : 03072017_NDOM_H_All_renum.pdb > The variable ion_ids is : [9749] > The variable ion_mol2files is : ['ZN_renum.mol2'] > The variable group_name is : NDOM > The variable cut_off is : 2.8 > The variable ionchg_fixation is : 0 > The variable gau_version is : g03 > The variable sqm_opt is : 0 > The variable force_field is : ff14SB > The variable gaff is : 1 > The variable frcmodfs is : [] > The variable naa_mol2files is : ['WAT.mol2'] > The variable water_model is : TIP3P > The variable ion_paraset is : CM (Only for nonbonded model) > The variable ion_info is : [] > ****************************************************************** > * * > *===================Generate the Initial frcmod file=============* > * * > ****************************************************************** > Atoms which has changed the atom types: [5694, 5750, 6151, 9749, 9750] > 361-HID.5694-NE2 : NB --> X1 > 365-HID.5750-NE2 : NB --> X2 > 389-GLU.6151-OE1 : O2 --> X3 > 613-ZN.9749-ZN : ZN --> Z1 > 614-WAT.9750-O : OW --> X4 > ==================Using the Seminario method to solve the problem. > Traceback (most recent call last): > File "/apps/chpc/chem/amber/14/bin/MCPB.py", line 434, in <module> > g0x) > File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py", > line 306, in gene_by_QM_fitting_sem > 'Int Atom Types') > File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/pymsmtmol/gauio.py", > line 47, in get_crds_from_fchk > crds.append(float(j)) > ValueError: could not convert string to float: Force > > Any advice on how to solve this would be greatly appreciated! > > Kind regards > > Lizelle Lubbe > > PhD (Medical biochemistry) candidate > Department of Integrative Biomedical Sciences > University of Cape Town > Disclaimer - University of Cape Town This e-mail is subject to UCT > policies and e-mail disclaimer published on our website at > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 > 21 650 9111. If this e-mail is not related to the business of UCT, it is > sent by the sender in an individual capacity. Please report security > incidents or abuse via csirt.uct.ac.za > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jul 04 2017 - 07:30:04 PDT