From owner-chemistry@ccl.net Fri Oct 28 01:52:00 2016 From: "Andreas Klamt klamt%x%cosmologic.de" To: CCL Subject: CCL: COSMO-RS calculations Message-Id: <-52466-161028015013-26287-up8sq4Sww+3xLge/1mgXww(_)server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-15 Date: Fri, 28 Oct 2016 07:50:01 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt|cosmologic.de] Hi Mishka, the title of your CCL entry was about "COSMO calculations", but the content was about COSMO-RS. Please note the fundamental difference!!! COSMO-RS is a statistical thermodynamics of interacting surfaces based on the polarization charge densities resulting from a COSMO calculation. COSMO-RS in its COSMOtherm implementation currently is most likely the most accurate way to calculate solvation free energies and hence free energy differences of molecules between different solvents, including mixtures and variable temperature. There are several remakes of COSMO-RS: The so-called COSMO-SAC, which is available for free at some Virginiatech web site in a really old version. I guess that version requires DMol/COSMo files as input. A newer version is available within the ADF-COSMO-RS module. In a recent benchmark by van der Spoel this yielded an RMSD of 2.3 kcal/mol on a dataset on which our COSMOtherm yields 1.7 kcal/mol. There is a COSMO-RS(Ol) available from DDBST GmbH, but hardly anybody has been using that. These are the implementations I am aware of. Best regards Andreas Am 27.10.2016 um 18:43 schrieb Mishka Alubinov mishkaalubinov*_*icloud.com: > Sent to CCL by: "Mishka Alubinov" [mishkaalubinov*_*icloud.com] > Dear All, > > is there any software except cosmologic to perform COSMORS calculation? > > > Best regards > Mishka.> > > -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt.:.cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Fri Oct 28 10:29:01 2016 From: "Maria khan mariabiochemist1]-[gmail.com" To: CCL Subject: CCL: MD Simulation by gromacs Message-Id: <-52467-161028065626-10606-Ye3ekbgc27q4UYy90acDrA.:.server.ccl.net> X-Original-From: "Maria khan" Date: Fri, 28 Oct 2016 06:56:25 -0400 Sent to CCL by: "Maria khan" [mariabiochemist1###gmail.com] Hello dear gromacs users.. I am running simulation for protein ligand complex that are Glutamate racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting atoms.For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt(it might for instance have been H3, and we only expected H1 & H2).Note that hydrogens might have been added to the entry for the N-terminus.Remove this hydrogen or choose a different protonation state to solve it.Option -ignh will ignore all hydrogens in the input."for making pdb2gmx and it doesnt form topology file. where am i doing wrong. kindly help me out. Regards and thanks From owner-chemistry@ccl.net Fri Oct 28 12:48:00 2016 From: "Elvis Martis elvis_bcp- -elvismartis.in" To: CCL Subject: CCL: MD Simulation by gromacs Message-Id: <-52468-161028115644-16936-A9w1nKfjoFhCuNa5SZBjKA|a|server.ccl.net> X-Original-From: Elvis Martis Content-Type: multipart/alternative; boundary=001a114d767a16f6f5053feee73a Date: Fri, 28 Oct 2016 21:26:15 +0530 MIME-Version: 1.0 Sent to CCL by: Elvis Martis [elvis_bcp/./elvismartis.in] --001a114d767a16f6f5053feee73a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi, How did you built the topology for the inhibitor? Regards *Elvis Martis* PhD Student, Bombay College of Pharmacy [image: photo] Email: elvis_bcp]^[elvismartis.in Website: http://www.elvismartis.in group website: http://www.profeccoutinho.net.in/ Address: =E2=80=8B Kalina, Santa Cruz [E] =E2=80=8B, Mumbai, 400 098, INDIA=E2=80=8B Alt. e-mail: emartis12]^[live.com On 28 October 2016 at 16:26, Maria khan mariabiochemist1]-[gmail.com < owner-chemistry]^[ccl.net> wrote: > > Sent to CCL by: "Maria khan" [mariabiochemist1###gmail.com] > Hello dear gromacs users.. > I am running simulation for protein ligand complex that are Glutamate > racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in > residue HIS 61 was not found in rtp entry HISB with 12 atoms while sortin= g > atoms.For a hydrogen, this can be a different protonation state, or it > might have had a different number in the PDB file and was rebuilt(it migh= t > for instance have been H3, and we only expected H1 & H2).Note that > hydrogens might have been added to the entry for the N-terminus.Remove > this hydrogen or choose a different protonation state to solve it.Option > -ignh will ignore all hydrogens in the input."for making pdb2gmx and it > doesnt form topology file. > where am i doing wrong. > kindly help me out. > Regards and thanks > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a114d767a16f6f5053feee73a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,
How did you built the topology for the inhibito= r?


=
Regards
=
Elvis Martis=C2=A0=C2=A0=C2=A0PhD St= udent, Bombay College of Pharmacy
3D"photo"= Em= ail:=C2=A0elvis= _bcp]^[elvismartis.in
Website:=C2=A0ht= tp://www.elvismartis.in
group website= :=C2=A0http= ://www.profeccoutinho.net.in/
Address:=C2=A0
=E2=80=8B
=C2=A0<= /font>Kalina, Santa Cruz [E]
=E2=80=8B, Mumbai, 400 098, INDIA=E2=80=8B

Alt. e-mail:=C2=A0em= artis12]^[live.com


On 28 October 2016 at 16:26, Maria khan mari= abiochemist1]-[gmail.com <owner-che= mistry]^[ccl.net> wrote:

Sent to CCL by: "Maria=C2=A0 khan" [mariabiochemist1###gmail.com]
Hello dear=C2=A0 gromacs users..
I am running simulation for protein ligand complex that are Glutamate
racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in<= br> residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting<= br> atoms.For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt(it might<= br> for instance have been H3, and we only expected H1 & H2).Note that
hydrogens might have been added to the entry for the N-terminus.Remove
this hydrogen or choose a different protonation state to solve it.Option -ignh will ignore all hydrogens in the input."for making pdb2gmx and i= t
doesnt form topology file.
where am i doing wrong.
kindly help me out.
Regards and thanks



-=3D This is automatically added to each message by the mailing script =3D-=
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--001a114d767a16f6f5053feee73a-- From owner-chemistry@ccl.net Fri Oct 28 13:23:00 2016 From: "Chandan Choudhury iitdckc:gmail.com" To: CCL Subject: CCL: MD Simulation by gromacs Message-Id: <-52469-161028115645-16850-F7JWvtaVvBygSrJ0Tcblwg/a\server.ccl.net> X-Original-From: Chandan Choudhury Content-Type: multipart/alternative; boundary=001a1147c8e4bc3b9c053feee628 Date: Fri, 28 Oct 2016 11:56:08 -0400 MIME-Version: 1.0 Sent to CCL by: Chandan Choudhury [iitdckc(a)gmail.com] --001a1147c8e4bc3b9c053feee628 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Maria, You need to first confirm the protonation state of HIS residues for your system. Then look at the residues in the rtp file and rename the HIS residues (in you pdb/gro) file and then run the pdb2gmx command. It is better you send the gromacs related messages to the gromacs mailing list. You might end up help from others also. Chandan On Fri, Oct 28, 2016 at 6:56 AM, Maria khan mariabiochemist1]-[gmail.com < owner-chemistry : ccl.net> wrote: > > Sent to CCL by: "Maria khan" [mariabiochemist1###gmail.com] > Hello dear gromacs users.. > I am running simulation for protein ligand complex that are Glutamate > racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in > residue HIS 61 was not found in rtp entry HISB with 12 atoms while sortin= g > atoms.For a hydrogen, this can be a different protonation state, or it > might have had a different number in the PDB file and was rebuilt(it migh= t > for instance have been H3, and we only expected H1 & H2).Note that > hydrogens might have been added to the entry for the N-terminus.Remove > this hydrogen or choose a different protonation state to solve it.Option > -ignh will ignore all hydrogens in the input."for making pdb2gmx and it > doesnt form topology file. > where am i doing wrong. > kindly help me out. > Regards and thanks > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Chandan Kumar Choudhury Post Doctoral Fellow Clemson University South Carolina USA *"All work and no play makes Jack a dull boy...=E2=80=9D* --001a1147c8e4bc3b9c053feee628 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Maria,
You need to first confirm the proto= nation state of HIS residues for your system. Then look at the residues in = the rtp file and rename the HIS residues (in you pdb/gro) file and then run= the pdb2gmx command.

It is better you send the gromacs relate= d messages to the gromacs mailing list. You might end up help from others a= lso.

Chandan=C2=A0

On Fri, Oct 28, 2016 at 6:56 AM, Maria khan mariab= iochemist1]-[gmail.com &= lt;owner-chemi= stry : ccl.net> wrote:

Sent to CCL by: "Maria=C2=A0 khan" [mariabiochemist1###gmail.com]
Hello dear=C2=A0 gromacs users..
I am running simulation for protein ligand complex that are Glutamate
racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in<= br> residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting<= br> atoms.For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt(it might<= br> for instance have been H3, and we only expected H1 & H2).Note that
hydrogens might have been added to the entry for the N-terminus.Remove
this hydrogen or choose a different protonation state to solve it.Option -ignh will ignore all hydrogens in the input."for making pdb2gmx and i= t
doesnt form topology file.
where am i doing wrong.
kindly help me out.
Regards and thanks



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY : ccl.n= et or use:
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--

Chandan Kumar Choudhury
Post Doctoral= Fellow
Clemson University
South Carolina
USA

"= All work and no play makes Jack a dull boy...=E2=80=9D

<= /div>
--001a1147c8e4bc3b9c053feee628--