[gmx-users] No default Ryckaert-Bell. types for proline

Wed Jun 3 02:51:26 CEST 2015

Thanks Justin,

I'm sorry that I'm not clear with what do you mean by "so you can likely
just use the same parameters in ffbonded.itp for this dihedral in the
zwitterionic form".

Also as I have mentioned before, when I look into the line 161, it refers
to a dihedral term concerning (CD N CA C) which is not able to be found in
ffbonded.itp. However, other dihedral terms such as (CD N CA CB) or (CD N
CA HA) which are also not found in itp do not report such error and I was
successful to grompp after commenting out the line 161. So why would this
happen?

Thanks in advance,
Kevin

On 2 Jun, 2015, at 20:05, Justin Lemkul <jalemkul at vt.edu
<javascript:_e(%7B%7D,'cvml','jalemkul at vt.edu');>> wrote:

On 6/1/15 12:25 PM, Kevin C Chan wrote:

pdb2gmx command:

gmx_d pdb2gmx -f proline.pdb -ter > 15: (OPLS-AA/L all-atom force field

(2001 aminoacid dihedrals)) > 1: TIP4P  TIP 4-point, recommended > 1:

PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one

residue) > 1: PRO-ZWITTERION_COO- (only use with zwitterions containing

exactly one residue)

(I have also tried 4: ZWITTERION_NH3+ (only use with zwitterions containing

exactly one residue) but the result was the same)

Screen-out:

http://pastebin.com/CuMa7aZ7#

topology:

http://pastebin.com/FSbcFGYR

It appears that there are simply no parameters in the OPLS-AA force field
for this entity.  Whether or not this is because OPLS-AA doesn't officially
have parameters for it or they are just missing from the GROMACS
implementation is something you'd have to dig into, but largely it seems
that all dihedral parameters for the N- and C-terminal forms of PRO are all
the same, so you can likely just use the same parameters in ffbonded.itp
for this dihedral in the zwitterionic form.

-Justin

Thanks in advance,

Kevin

On Tue, Jun 2, 2015 at 12:11 AM, Justin Lemkul <jalemkul at vt.edu
<javascript:_e(%7B%7D,'cvml','jalemkul at vt.edu');>> wrote:

On 6/1/15 12:09 PM, Kevin C Chan wrote:

Thanks Justin,

I did not but I tried just now. The aforementioned dihedral terms remain

along with the errors.

Please provide your full pdb2gmx command, all screen output, and full

topology.  Use file sharing services, pastebin, etc. as needed.

-Justin

 Thanks in advance,

Kevin

On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul <jalemkul at vt.edu
<javascript:_e(%7B%7D,'cvml','jalemkul at vt.edu');>> wrote:

On 6/1/15 10:57 AM, Kevin C Chan wrote:

 Dear Users,

I am testing with OPLSSaa force-field of proline. First I arbitrarily

extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro

and

top are however not suitable for further grompp (even minimization). The

error messages are as follows:

ERROR 1 [file topol.top, line 161]:

    No default Ryckaert-Bell. types

When I look into the line 161, it refers to a dihedral term concerning

(CD

N CA C) which is not able to be found in ffbonded.itp. However, other

dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not

found in itp do not report such error and I was successful to grompp

after

commenting out the line 161.

Why would this happen?

 Did you choose the proper "PRO-ZWITTERION-*" termini when running

pdb2gmx?

-Justin

--

==================================================

Justin A. Lemkul, Ph.D.

Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences

School of Pharmacy

Health Sciences Facility II, Room 629

University of Maryland, Baltimore

20 Penn St.

Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu
<javascript:_e(%7B%7D,'cvml','jalemkul at outerbanks.umaryland.edu');> | (410)
706-7441

http://mackerell.umaryland.edu/~jalemkul

==================================================

--

Gromacs Users mailing list

* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit

https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

send a mail to gmx-users-request at gromacs.org
<javascript:_e(%7B%7D,'cvml','gmx-users-request at gromacs.org');>.

--

==================================================

Justin A. Lemkul, Ph.D.

Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences

School of Pharmacy

Health Sciences Facility II, Room 629

University of Maryland, Baltimore

20 Penn St.

Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu
<javascript:_e(%7B%7D,'cvml','jalemkul at outerbanks.umaryland.edu');> | (410)
706-7441

http://mackerell.umaryland.edu/~jalemkul

==================================================

--

Gromacs Users mailing list

* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit

https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

send a mail to gmx-users-request at gromacs.org
<javascript:_e(%7B%7D,'cvml','gmx-users-request at gromacs.org');>.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu
<javascript:_e(%7B%7D,'cvml','jalemkul at outerbanks.umaryland.edu');> | (410)
706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================
-- 
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-request at gromacs.org
<javascript:_e(%7B%7D,'cvml','gmx-users-request at gromacs.org');>.