Reading of charges from PRMTOP file and labeling atoms with charge value ?
Dear all, when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ? It seems to me that the recommended commands sequence focus labelopt info charge label works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file. Thanks a lot in advance for your comments ! Best wishes, Marek Maly -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Hi Marek, I just made some changes to preserve the prmtop charge info, so if you get tomorrow's daily build you will be able to use those charges. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 1, 2010, at 3:01 AM, Marek Maly wrote:
Dear all,
when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ?
It seems to me that the recommended commands sequence
focus labelopt info charge label
works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file.
Thanks a lot in advance for your comments !
Best wishes,
Marek Maly
Hi Eric, thanks a lot ! Did I understood well that in your new Chimera version I simply launch my PRMROP/INPCRD(RST,MDCRD) file, then use these command sequence: focus labelopt info charge label and the atoms will be labeled with charges from the PRMTOP file, without any necessity to use "Add Charge" routine before ? Thanks again ! Best wishes, Marek Dne Wed, 02 Jun 2010 00:35:03 +0200 Eric Pettersen <pett@cgl.ucsf.edu> napsal/-a:
Hi Marek, I just made some changes to preserve the prmtop charge info, so if you get tomorrow's daily build you will be able to use those charges.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 1, 2010, at 3:01 AM, Marek Maly wrote:
Dear all,
when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ?
It seems to me that the recommended commands sequence
focus labelopt info charge label
works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file.
Thanks a lot in advance for your comments !
Best wishes,
Marek Maly
__________ Informace od ESET NOD32 Antivirus, verze databaze 5164 (20100601) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Yes, that is correct. --Eric On Jun 1, 2010, at 3:37 PM, Marek Maly wrote:
Hi Eric, thanks a lot !
Did I understood well that in your new Chimera version I simply launch my PRMROP/INPCRD(RST,MDCRD) file, then use these command sequence:
focus labelopt info charge label
and the atoms will be labeled with charges from the PRMTOP file, without any necessity to use "Add Charge" routine before ?
Thanks again !
Best wishes,
Marek
Dne Wed, 02 Jun 2010 00:35:03 +0200 Eric Pettersen <pett@cgl.ucsf.edu> napsal/-a:
Hi Marek, I just made some changes to preserve the prmtop charge info, so if you get tomorrow's daily build you will be able to use those charges.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 1, 2010, at 3:01 AM, Marek Maly wrote:
Dear all,
when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ?
It seems to me that the recommended commands sequence
focus labelopt info charge label
works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file.
Thanks a lot in advance for your comments !
Best wishes,
Marek Maly
__________ Informace od ESET NOD32 Antivirus, verze databaze 5164 (20100601) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
OK, thank you very much for this improvement ! Best wishes, Marek Dne Wed, 02 Jun 2010 01:09:44 +0200 Eric Pettersen <pett@cgl.ucsf.edu> napsal/-a:
Yes, that is correct.
--Eric
On Jun 1, 2010, at 3:37 PM, Marek Maly wrote:
Hi Eric, thanks a lot !
Did I understood well that in your new Chimera version I simply launch my PRMROP/INPCRD(RST,MDCRD) file, then use these command sequence:
focus labelopt info charge label
and the atoms will be labeled with charges from the PRMTOP file, without any necessity to use "Add Charge" routine before ?
Thanks again !
Best wishes,
Marek
Dne Wed, 02 Jun 2010 00:35:03 +0200 Eric Pettersen <pett@cgl.ucsf.edu> napsal/-a:
Hi Marek, I just made some changes to preserve the prmtop charge info, so if you get tomorrow's daily build you will be able to use those charges.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 1, 2010, at 3:01 AM, Marek Maly wrote:
Dear all,
when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ?
It seems to me that the recommended commands sequence
focus labelopt info charge label
works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file.
Thanks a lot in advance for your comments !
Best wishes,
Marek Maly
__________ Informace od ESET NOD32 Antivirus, verze databaze 5164 (20100601) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
--Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
__________ Informace od ESET NOD32 Antivirus, verze databaze 5164 (20100601) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
participants (2)
-
Eric Pettersen -
Marek Maly