From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Nov 01 2005 - 13:21:22 CST
What you can do (as in previous messages) is to CAREFULLY copy the topology and parameters from the stream files and paste them in your parent files. This is dangerous, though, because you can contaminate your parent files and you can lose the track of what you're doing.
The other thing I suggested before is to "invoke" the stream files you need as if you are reading the normal *.inp file. For example, in your psfgen file you'll write something like:
topology your_parent_file.inp
topology your_stream_file.str
and the rest of your parameters according to what you want to get. I haven't tried that, but hopefuly it'll help.
Good luck!
Michel
________________________________
From: Grace Shen [mailto:Lingling.Shen_at_bnpi.com]
Sent: Tue 11/1/2005 10:15 AM
To: Michel Espinoza-Fonseca; Grace Shen; NAMD Users List
Subject: RE: namd-l: About ADP
Thank you.
Then could you tell me how can I use that stream file in NAMD? Maybe I should edit the topology and params files, adding the 'patch' from stream file?
Then what should be pasted into topology file and what should be pasted into parameters file?
Thanks,
Grace
-----Original Message-----
From: Michel Espinoza-Fonseca [mailto:mef_at_ddt.biochem.umn.edu]
Sent: Tuesday, November 01, 2005 10:17 AM
To: Grace Shen; NAMD Users List
Subject: RE: namd-l: About ADP
Topology and parameter files for ADP are located in the stream files folder. There you can find the files you need.
________________________________
From: owner-namd-l_at_ks.uiuc.edu on behalf of Grace Shen
Sent: Tue 11/1/2005 9:48 AM
To: NAMD Users List
Subject: namd-l: About ADP
Dear All:
I searched the web and found that a lot of people said that top_all27_prot_na.inp and par_all27_prot_na.inp files have parameters for ADP. I only can found top_all27_prot_na.rtf and par_all27_prot_na.prm files from Alex Mackerell's homepage. But there is no "ADP" information in these two files.
Could someone please tell me what happened and how can I get ADP force field parameters?
Thanks,
Grace
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