VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Mon Jul 30 2012 - 17:32:45 CDT

Hi John,

Glad to hear you're on top of it - I had a feeling you would be! For the record, I'm using the VMD 1.9 official release.

Cheers,

Tristan

 
 
Tristan Croll
Lecturer
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
 
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On 31/07/2012, at 7:25 AM, "John Stone" <johns_at_ks.uiuc.edu> wrote:

> Hi Tristan,
> There's an ongoing issue with the combination of the new
> CGENFF atom parameters and the standard versions of the PSF file format.
> You didn't say which version of VMD you're using, but you would need to
> use the latest test versions of VMD to get around this problem. The
> root cause is that the standard versions of the PSF file format have
> Fortran-based fix-field-width formats, that do not allow arbitrary-length
> data. NAMD has been able to ignore the standard PSF formatting rules and
> just accept anything that's a space delimited file, since it only reads
> PSF files that come from a handful of sources all of which can generate
> such files. VMD on the other hand, has to be rigorous and correctly parse
> all of the non-NAMD file formats, and so if your PSF file doesn't have a
> special "NAMD" tag in its header, the VMD PSF plugin will restrict the parsing
> to the legal field widths, which will end up truncating your atom data.
> If you use the latest test versions of VMD/NAMD/psfgen, this problem should
> be solved already by generating PSF files that have this special "NAMD" tag
> in them (the NAMD tag denotes the use of the space-delimited free-format
> field widths that NAMD accepts, but that are incompatible with the standard
> PSF file format specs).
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Jul 29, 2012 at 10:53:08AM +1000, Tristan Croll wrote:
>> Hi,
>>
>>
>>
>> I've been running a few simulations involving a small molecule
>> (sphingosylphosphorylcholine, SPC) parameterised using the ParamChem
>> server. The simulations I've just started running have the amine group on
>> SPC deprotonated. When visualising this, I got something of a shock when
>> I asked VMD to colour the atoms by charge - it was reporting the charge on
>> each of the two amine hydrogens as +2.0.
>>
>>
>>
>> Reassuringly, the charges in the stream file are fine:
>>
>>
>>
>> ATOM N51 NG321 -0.987 ! 22.978
>>
>> ATOM H511 HGPAM2 0.341 ! 1.518
>>
>> ATOM H512 HGPAM2 0.341 ! 1.518
>>
>>
>>
>> ... as are those in the AutoPSF-generated PSF file:
>>
>>
>>
>> 9197 O2 153 SPUD N51 NG321 -0.987000 14.0070 0
>>
>> 9198 O2 153 SPUD H511 HGPAM2 0.341000 1.0080 0
>>
>> 9199 O2 153 SPUD H512 HGPAM2 0.341000 1.0080 0
>>
>>
>>
>> The NAMD output also reports the total system charge correctly:
>>
>>
>>
>> Info: TOTAL CHARGE = 6.65523e-06 e
>>
>>
>>
>> VMD reports the atom types as "HGPA" - my guess is that the parser only
>> allows four characters for the atom type, so when fed HGPAM2 has ignored
>> the M and taken 2 as the charge.
>>
>>
>>
>> Cheers,
>>
>>
>>
>> Tristan
>>
>>
>>
>> Tristan Croll
>>
>> Lecturer
>>
>> Faculty of Health
>>
>> Institute of Health and Biomedical Engineering
>>
>> Queensland University of Technology
>>
>> 60 Musk Ave
>>
>> Kelvin Grove QLD 4059 Australia
>>
>> +61 7 3138 6443
>>
>>
>>
>> This email and its attachments (if any) contain confidential information
>> intended for use by the addressee and may be privileged. We do not waive
>> any confidentiality, privilege or copyright associated with the email or
>> the attachments. If you are not the intended addressee, you must not use,
>> transmit, disclose or copy the email or any attachments. If you receive
>> this email by mistake, please notify the sender immediately and delete the
>> original email.
>>
>>
>>
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078