VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sat Nov 05 2016 - 18:30:33 CDT

The problem is your resname of 00 (zero zero). This screws up the atomselection. It can be handled by putting it in quotes ( \”00\”), but will likely cause trouble throughout FFTK and other plugins. The easiest solution is to give it a different name in your input PSF and PDB.

Best,
JC

> On Nov 2, 2016, at 12:27 PM, Eisenhart, Andrew (eisenhaw) <eisenhaw_at_mail.uc.edu> wrote:
>
> Just checked again and the taget data section does parse the individual O15 files correctly. I even get the same error when using just one of the O15 files so I think the problem is more general. The also the pdb and the psf files are on the second page of the chargeOpt folder.
>
> -Thanks
> Andrew
> From: JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>>
> Sent: Tuesday, November 01, 2016 3:39:40 PM
> To: Christopher G Mayne
> Cc: Eisenhart, Andrew (eisenhaw); vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: FFTK measure bond error
>
> Oh yeah, check these things first. If you’re still stuck, let us know.
>
> Thanks Chris!
> JC
>
>> On Nov 1, 2016, at 11:45 AM, Mayne, Christopher G <cmayne2_at_illinois.edu <mailto:cmayne2_at_illinois.edu>> wrote:
>>
>> Andrew,
>>
>> I’m going to need the PSF and geometry optimized PDB file in order to try to reproduce your error. However, I already have one suspicion: when you load in the Gaussian target data, the parser attempts to assign the atom name based on the file name. In older versions of ffTK (I’m pretty sure that I changed this), when scanning multiple angles for carbonyls, the parsed atom name is e.g., O15-120a rather than O15. Make sure that you double check the atom name assignment in the QM Target Data section.
>>
>> Regards,
>> Christopher Mayne
>>
>>> On Oct 31, 2016, at 9:38 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>>>
>>> I will take a look soon. Please bug me personally if you don’t hear anything within a couple days.
>>>
>>> Best,
>>> JC
>>>
>>>> On Oct 31, 2016, at 2:15 PM, Eisenhart, Andrew (eisenhaw) <eisenhaw_at_mail.uc.edu <mailto:eisenhaw_at_mail.uc.edu>> wrote:
>>>>
>>>> Hello,
>>>>
>>>> I am attempting to complete the charge optimization for a fragment of my molecule using VMD-fftk (1.9.2). I am receiving the following error code when running the optimization.
>>>>
>>>>
>>>> measure bond: must specify exactly two atoms in a list
>>>> measure bond: must specify exactly two atoms in a list
>>>> while executing
>>>> "measure bond "[$temp1 get index] [$temp2 get index]" frame $i"
>>>> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 215)
>>>> invoked from within
>>>> "::ForceFieldToolKit::ChargeOpt::optimize"
>>>> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
>>>> invoked from within
>>>> "::ForceFieldToolKit::gui::coptRunOpt "
>>>> invoked from within
>>>> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
>>>> invoked from within
>>>> ".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
>>>> (command bound to event)
>>>>
>>>> There are few similar questions on the mailing list already, but no solutions that have worked for me. I've tried simulated annealing and downhill with no success.
>>>>
>>>> I can replicate the error when loading as few as one log file.
>>>>
>>>> Here is a link to my box folder that contains my .log and other initial files. https://uc.box.com/s/3vye3uqw8d90vpqyn0qgm08k4s5sgf18 <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_3vye3uqw8d90vpqyn0qgm08k4s5sgf18&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=P1kBONdiuIUOjtm29TKzU2sVUpYAuHXL8fRv9R10oBI&e=>
>>>> This folder contains the Gaussian input files i used to generate the log files. https://uc.box.com/s/udepalaygv1sq2xqwwka9ox10vl3mr5j <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_udepalaygv1sq2xqwwka9ox10vl3mr5j&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=oiUjKnxEn4NwtDxvAK7bv99ogAj2OJo8ZyzloLtRUpw&e=>
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_ku0ujld45bjirmut8xbelcxlukuhoq42&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=es8HyFikXoG8quIaeQhLX5_TtM8U1Zoygt2rSHqzjco&e=> <https://urldefense.proofpoint.com/v2/url?u=https-3A__uc.box.com_s_3vye3uqw8d90vpqyn0qgm08k4s5sgf18&d=DQMF-g&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=F5kKc5Rhmmlee4S-dJMey3-z8c6aer0EfW-sSkEaAJ0&s=P1kBONdiuIUOjtm29TKzU2sVUpYAuHXL8fRv9R10oBI&e=>
>>>> Thanks for your time!
>>>>
>>>>
>>>> -Andrew Eisenhart