From owner-chemistry@ccl.net Mon Feb 5 10:13:00 2024 From: "Obinna Eugene Onyemaobi obinna2022++nanoctr.cn" To: CCL Subject: CCL: forcefield issues Message-Id: <-55096-240205035730-20754-o+NvvOKiLTeair8dvFt/Jg[a]server.ccl.net> X-Original-From: "Obinna Eugene Onyemaobi" Content-Type: multipart/alternative; boundary="----=_Part_10203_1261472070.1707123425389" Date: Mon, 5 Feb 2024 16:57:05 +0800 (GMT+08:00) MIME-Version: 1.0 Sent to CCL by: "Obinna Eugene Onyemaobi" [obinna2022===nanoctr.cn] ------=_Part_10203_1261472070.1707123425389 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 SGkgQW1iZXIsCgoKCgpJIHRydXN0IG15IG1haWwgbWVldHMgeW91IHdlbGwuCgoKCgpJIGhhdmV0 d28gbWFqb3IgcHJvYmxlbXMgYW5kIGkgbmVlZCBoZWxwIHdpdGggaXQuCgoKCgpGaXJzdGx5LCBp cyB0aGVyZSBhIHRsZWFwIHNjcmlwdCBvbiBob3cgaSBjYW4gdXNlIGNoYXJtbTM2bSBmb3JjZWZp ZWxkIGluIGFtYmVyIHRvIGdlbmVyYXRlIHRvcG9sb2d5IGFuZCBwYXJhbXRlciBmaWxlcyBmb3Ig cHJvdGVpbi4gaWYgeWVzLCBwbGVhc2Uga2luZGx5IHNlbmQgdG8gbWUuCgoKCgpTZWNvbmRseSwg aG93IGNhbiBpIGdlbmVyYXRlIG5vbi1zb2x2YXRlZCB0b3BvbG9neSBhbmQgcGFyYW1ldGVyIGZp bGUgdXNpbmcgY2hhcm1tMzZtIGZvcmNlZmllbGQgaW4gYW1iZXIuIGkgYWxzbyBuZWVkIGEgc2Ny aXB0IGZvciB0aGF0IHRvby4KCgoKClRoYW5rIHlvdSwKCgoKCk9iaW5uYS4KCkJlaWppbmcsIENo aW5h ------=_Part_10203_1261472070.1707123425389 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 PHA+CglIaSBBbWJlciwKPC9wPgo8cD4KCTxicj4KPC9wPgo8cD4KCUkgdHJ1c3QgbXkgbWFpbCBt ZWV0cyB5b3Ugd2VsbC4KPC9wPgo8cD4KCTxicj4KPC9wPgo8cD4KCUkgaGF2ZXR3byBtYWpvciBw cm9ibGVtcyBhbmQgaSBuZWVkIGhlbHAgd2l0aCBpdC4KPC9wPgo8cD4KCTxicj4KPC9wPgo8cD4K CUZpcnN0bHksIGlzIHRoZXJlIGEgdGxlYXAgc2NyaXB0IG9uIGhvdyBpIGNhbiB1c2UgY2hhcm1t MzZtIGZvcmNlZmllbGQgaW4gYW1iZXIgdG8gZ2VuZXJhdGUgdG9wb2xvZ3kgYW5kIHBhcmFtdGVy IGZpbGVzIGZvciBwcm90ZWluLiBpZiB5ZXMsIHBsZWFzZSBraW5kbHkgc2VuZCB0byBtZS4KPC9w Pgo8cD4KCTxicj4KPC9wPgo8cD4KCVNlY29uZGx5LCBob3cgY2FuIGkgZ2VuZXJhdGUgbm9uLXNv bHZhdGVkIHRvcG9sb2d5IGFuZCBwYXJhbWV0ZXIgZmlsZSB1c2luZyBjaGFybW0zNm0gZm9yY2Vm aWVsZCBpbiBhbWJlci4gaSBhbHNvIG5lZWQgYSBzY3JpcHQgZm9yIHRoYXQgdG9vLgo8L3A+Cjxw PgoJPGJyPgo8L3A+CjxwPgoJVGhhbmsgeW91LAo8L3A+CjxwPgoJPGJyPgo8L3A+CjxwPgoJT2Jp bm5hLgo8L3A+CjxwPgoJQmVpamluZywgQ2hpbmEKPC9wPg== ------=_Part_10203_1261472070.1707123425389-- From owner-chemistry@ccl.net Mon Feb 5 12:39:01 2024 From: "David A Case dacase1(!)gmail.com" To: CCL Subject: CCL: forcefield issues Message-Id: <-55097-240205115539-25758-G2I2UOVpjHvRBitc8oubMQ^_^server.ccl.net> X-Original-From: David A Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii; format=flowed Date: Mon, 5 Feb 2024 09:55:29 -0700 MIME-Version: 1.0 Sent to CCL by: David A Case [dacase1*gmail.com] On Mon, Feb 05, 2024, Obinna Eugene Onyemaobi obinna2022++nanoctr.cn wrote: > >Firstly, is there a tleap script on how i can use charmm36m forcefield in >amber to generate topology and paramter files for protein. if yes, please >kindly send to me. > >Secondly, how can i generate non-solvated topology and parameter file using >charmm36m forcefield in amber. i also need a script for that too. First, questions about Amber are best addressed to its mailing list. See http://lists.ambermd.org/mailman/listinfo/amber for information on how to subscribe. Second, tleap in Amber doesn't directly allow access to CHARMM force fields. I'd recommend the CHARMM-GUI, which can prepare Amber-compatible files: https://www.charmm-gui.org/. regards...dave case From owner-chemistry@ccl.net Mon Feb 5 15:59:00 2024 From: "Monsurat M. Lawal lawalmonsurat635=gmail.com" To: CCL Subject: CCL: forcefield issues Message-Id: <-55098-240205131351-11812-LyfSOwUtV2vChj9+FXN97g*|*server.ccl.net> X-Original-From: "Monsurat M. Lawal" Content-Type: multipart/alternative; boundary="000000000000d8d5140610a66b4c" Date: Mon, 5 Feb 2024 13:13:04 -0500 MIME-Version: 1.0 Sent to CCL by: "Monsurat M. Lawal" [lawalmonsurat635#gmail.com] --000000000000d8d5140610a66b4c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Obinna, Your question is better suited to the AMBER mailing list than CCL (personal opinion). See the conversation here (http://archive.ambermd.org/201702/0339.html) Like in the conversation, you can generate your input file with CHARMM-GUI https://www.charmm-gui.org/, and it is user-friendly and open (register with your academic email). Regards Monsurat. On Mon, Feb 5, 2024 at 11:56=E2=80=AFAM Obinna Eugene Onyemaobi obinna2022+= + nanoctr.cn wrote: > Hi Amber, > > > I trust my mail meets you well. > > > I havetwo major problems and i need help with it. > > > Firstly, is there a tleap script on how i can use charmm36m forcefield in > amber to generate topology and paramter files for protein. if yes, please > kindly send to me. > > > Secondly, how can i generate non-solvated topology and parameter file > using charmm36m forcefield in amber. i also need a script for that too. > > > Thank you, > > > Obinna. > > Beijing, China > --000000000000d8d5140610a66b4c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Obinna,
Your question is better suited to the AMBER= mailing list than CCL (personal opinion).
See the conversation= =C2=A0here (http://archive.ambermd.org/201702/0339.html)
Like= in the conversation, you can generate your input file with CHARMM-GUI=C2= =A0https://www.ch= armm-gui.org/, and it is user-friendly and open (register with your aca= demic email).

Regards
Monsurat.=C2=A0

On Mon, Feb 5, 2024 at 11:56=E2=80=AFAM O= binna Eugene Onyemaobi obinna2022++nanoctr.cn= <owner-chemistry---ccl.net= > wrote:
=

Hi Amber,


I trust my mail meets you well.


I havetwo major problems and i need help with it.


Firstly, is there a tleap script on how i can use charmm36m forcefield in = amber to generate topology and paramter files for protein. if yes, please k= indly send to me.


Secondly, how can i generate non-solvated topology and parameter file usin= g charmm36m forcefield in amber. i also need a script for that too.


Thank you,


Obinna.

Beijing, China

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