VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Apr 23 2018 - 10:51:27 CDT

Hi Fan,

Could you also send along the parameter file you are trying to use? From what you've provided, this should totally have worked if the parameter is in CHARMM format, so I'd like to try it for myself to see where the script is going wrong.

-Josh

On 2018-04-23 08:16:39-06:00 fan li wrote:

Hi Josh
I have loaded the psf file. And I also checked the "type" filed, and it does contain atom type. Although the psf is not originally generated by vmd, so I think vmd can still handle it as long as vmd can read it. I could not find any problems, so I have attached psf I used. Would you mind trying it and telling me what is wrong?
Thanks
Fan Li

2018-04-21 19:52 GMT+01:00 Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>>:
Hi Fan,

Did you load the psf first? topotools isn't doing anything magic, it is just matching what VMD has stored internally in the "type" field, which is not set correctly if you only load a pdb, since it does not contain type information! To correctly load the system, load the psf first, and then (optionally), the pdb. Have you also checked the contents of your psf file? It may also be that you created it in such a way that it does not have atomtype information contained within it.

-Josh

On 2018-04-21 08:31:59-06:00 owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> wrote:

Hi everyone
I am using the topo writegmxtop to conver the psf file to top file. The command I used is "topo writegmxtop my.top [list parameterfile1.prm]". The angles and dihedrals are correct, but the "type" column in atoms directive is same as the "atom" column (I mean C1, C2 are the labels for the "atom", but it should be same label as the one in the forcefiled in the "type" column ,but it is not in my case). The atom type is already in my psf file and parameterfile1.prm file, and there is no errors and warnings during the conversion.
Is there something wrong or it the right result?
Fan Li