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Re: c36a4 topology file changed
lennart #23529 02/26/10 12:45 AM
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lqz Offline OP
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Thanks for your hint. In fact, some residues are not defined in the new topology file. So I copied some of the parameters from the old edition to the new edition. That caused some ambiguity, especially in the par file. I rearranged the order of the copied part and the default part in the par file. Now the warnings are gone. I only got following message when reading the rtf files:

CHARMM> OPEN READ UNIT 2 CARD NAME ./top_all22_prot-all.inp
VOPEN> Attempting to open::./top_all22_prot-all.inp::
OPNLGU> Unit 2 opened for READONLY access to /home/lxz79/charmm-test/./top_all22_prot-all.inp

CHARMM> READ RTF UNIT 2 CARD
MAINIO> Residue topology file being read from unit 2.
TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *

CHARMM> CLOSE UNIT 2
VCLOSE: Closing unit 2 with status "KEEP"

CHARMM>

CHARMM> !
CHARMM> !Read nucleo-acid parameters
CHARMM> !
CHARMM> OPEN READ UNIT 2 CARD NAME ./par_all22_prot-all.inp
VOPEN> Attempting to open::./par_all22_prot-all.inp::
OPNLGU> Unit 2 opened for READONLY access to /home/lxz79/charmm-test/./par_all22_prot-all.inp

CHARMM> READ PARAM UNIT 2 CARD

PARAMETER FILE BEING READ FROM UNIT 2
TITLE> *>>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

The last line showed that NONBOND, HBOND lists and IMAGE atoms cleared. Is that related to the par file? thanks a lot.

Re: c36a4 topology file changed
lqz #23531 02/26/10 07:09 AM
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That all seems OK, but random manipulation of rtf/parameter files may still lead to unreliable results.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: c36a4 topology file changed
lennart #23542 02/26/10 04:23 PM
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I only copied and pasted information that new topology files do not have but my proteins need. I do not know if there is other way to do it and make the results more trustable.

Re: c36a4 topology file changed
lqz #23544 02/26/10 04:31 PM
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Keep using the old files. Why do you need to use the new files?
Or find where the information is in the new set of files.
If the information is something that has been added locally it would have been a great help if you had told us about this in the first place.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: c36a4 topology file changed
lennart #23550 02/26/10 06:46 PM
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I think Lennart is on to something; this whole story just doesn't make sense. No changes have been made to the official protein topology file since the introduction of the CMAP term, which has been integrated in toppar/top_all22_prot.inp starting from C35. And those changes are additions, not deletions. And yes, I double-checked the c36a4 distribution. You must have been working with modified versions of those files that are internal to your lab (and hence outside of the scope of this forum).

Re: c36a4 topology file changed
Kenno #23554 02/26/10 08:13 PM
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You are right. I believe the extra residue definition part are internal to my lab only, for example, the gtp. Although I do not know where it originally came from. I just copied those parts to the new topology files since I could not find a better way to do.

Comparing the former and the new topology files, I could see that several parameters are updated. Since I am going to work on new projects and I believe the new charmm and topology files are better, I prefer to use new topology files.

Re: c36a4 topology file changed
lqz #23555 02/26/10 08:20 PM
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Unless your original files are very old I don't think there should be any significant parameter changes. How could they be only "slightly different from c36a4" if there are whole residues added locally?

Your habit of hiding (or providing misleading) information makes it very difficult to help you.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: c36a4 topology file changed
lqz #23556 02/26/10 08:49 PM
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Originally Posted By: lqz
Comparing the former and the new topology files, I could see that several parameters are updated. Since I am going to work on new projects and I believe the new charmm and topology files are better, I prefer to use new topology files.

When talking about the parameter file, you should say "parameter file", not "topology file".

Parameters were not updated with the addition of the CMAP term, only added. Either you're comparing against a really old (pre-2004) version of the parameter file, or people in your lab fiddled with the parameters. Either way, this is something you have to sort out with the people in your lab, not with the people on this forum.

Lastly, it cannot be guaranteed that the residues added by the people in your lab are compatible with the newer parameters.

Oh yeah, can a forum administrator move this thread to "parameter set discussion"? Thanks in advance! smile

Last edited by Kenno; 02/26/10 08:53 PM. Reason: Added two last sentences.
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