On 9/18/16 1:12 PM, Sameer Edirisinghe wrote:
Dear Dr. Justin,
Thanks for the reply. Following is the whole .rtp file i used. ( As you
said it was generated by using PRODRG)
You shouldn't use the charges from PRODRG. They assume a united-atom force
field, and are of very low quality. You can't force them into working with
OPLS-AA. It's fundamentally wrong.
If you want free help with a problem, you have to provide full information.
Fragments of .rtp files are not helpful and it's a waste of time for those who
are trying to give you advice.
[ bondedtypes ]
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1
; MDI
[ MD ]
[ atoms ]
CAY opls_135 0 1
CAX opls_135 0.048 2
CAW opls_135 0.047 2
CAV opls_135 0.144 2
OAU opls_154 -0.112 2
CAS opls_131 0.219 2
OAT opls_236 -0.41 2
NAO opls_900 0.073 2
HAO opls_250 -0.009 2
CAE opls_260 0.056 3
CAF opls_145 -0.018 3
HAF opls_140 0.004 3
CAA opls_145 -0.018 3
HAA opls_140 0.004 3
CAD opls_145 -0.018 3
HAD opls_140 0.004 3
CAC opls_145 -0.018 3
HAC opls_140 0.004 3
CAB opls_145 -0.022 4
CAG opls_071 0.044 4
CAH opls_145 -0.022 4
CAM opls_145 -0.008 5
HAM opls_140 0.008 5
CAL opls_145 -0.008 6
HAL opls_140 0.008 6
CAI opls_145 -0.008 7
HAI opls_140 0.008 7
CAJ opls_145 -0.008 8
HAJ opls_140 0.008 8
CAK opls_145 0.072 9
NAN opls_900 0.072 9
HAN opls_250 -0.009 9
CAP opls_131 0.214 9
OAQ opls_236 -0.419 9
OAR opls_154 -0.115 9
CAZ opls_135 0.14 9
CBA opls_135 0.045 9
CBB opls_135 0.01 10
CBC opls_135 -0.01 10
HA1 opls_140 -0.013 1
HA2 opls_140 -0.013 1
HA3 opls_140 -0.014 1
HAZ opls_140 -0.013 1
HA0 opls_140 -0.013 1
HAX opls_140 -0.013 1
HAY opls_140 -0.013 1
HAV opls_140 -0.013 1
HAW opls_140 -0.013 1
HAG opls_140 -0.013 1
HAH opls_140 -0.013 1
HA4 opls_140 -0.013 1
HA5 opls_140 -0.013 1
HBA opls_140 -0.013 1
HBB opls_140 -0.013 1
HBC opls_140 -0.013 1
HBD opls_140 -0.013 1
HBF opls_140 -0.013 1
HBG opls_140 -0.013 1
HBE opls_140 -0.013 1
[ bonds ]
CAY HA1
CAY HA2
CAY HA3
CAX CAY
CAX HAZ
CAX HA0
CAX CAW
CAW HAX
CAW HAY
CAW CAV
CAV HAV
CAV HAW
CAV OAU
CAS OAU
CAS OAT
CAS NAO
NAO HAO
CAE NAO
CAE CAF
CAE CAD
CAF HAF
CAF CAA
CAA HAA
CAB CAA
CAD HAD
CAD CAC
CAC HAC
CAB CAC
CAB CAG
CAG HAG
CAG HAH
CAH CAG
CAH CAM
CAH CAI
CAM HAM
CAM CAL
CAL HAL
CAK CAL
CAI HAI
CAI CAJ
CAJ HAJ
CAK CAJ
CAK NAN
NAN HAN
CAP NAN
CAP OAQ
CAP OAR
CAZ OAR
CAZ HA4
CAZ HA5
CAZ CBA
CBA HBA
CBA HBB
CBA CBB
CBB HBC
CBB HBD
CBB CBC
CBC HBF
CBC HBG
CBC HBE
ffbonded.itp file modified with the relevant bonds as below (part has
mentioned below)
CAY HA1 1 0.10900 284512.0 ;
CAY HA2 1 0.10900 284512.0 ;
CAY HA3 1 0.10900 284512.0 ;
CAX CAY 1 0.15220 265265.6 ;
CAX HAZ 1 0.10900 284512.0 ;
As I said before, you cannot use atom names in ffbonded.itp.
I know atom name is irrelevant but im bit confused how to write .rtp
without names for my 59 atom molecule.
The .rtp file *does* use atom names. See the manual. That part is fine. What
you cannot do is try to assign parameters using names. Those require types.
-Justin
regards
On Sun, Sep 18, 2016 at 10:09 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/18/16 12:30 PM, Sameer Edirisinghe wrote:
Dear users,
There is one thing i cannot clarify from gromacs manual which is about
following error occurred while running grompp
Fatal error:
Unknown bond_atomtype CAY
I used to create .rtp file from atom types which are already defined in
atomtype.atp file. But still above error occurring while running grompp.
Not sure should i add again thes atoms to atp file and if so how to add
them. Part of my rtp file is as below, I have modified the ffbonded.itp
(only bond types added) successfully.
What did you add to ffbonded.itp? Whatever it was is causing an error.
Based on the .rtp entry below, it looks like you tried to use atom names in
ffbonded.itp. That's not right. All interactions (bonded and nonbonded)
are defined by atom type. The name is irrelevant. If you're re-using only
OPLS-AA atom types, most of the bonded interactions should be present
already.
[ bondedtypes ]
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1
You're missing entries here if you're trying to create an OPLS-derived
force field. Look at oplsaa.ff/aminoacids.rtp
; MDI
[ MD ]
[ atoms ]
CAY opls_135 0.000 1
CAX opls_135 0.048 2
CAW opls_135 0.047 2
CAV opls_135 0.144 2
OAU opls_154 -0.112 2
This can't possibly be right. You've defined only heavy atoms (OPLS-AA is
an all-atom force field, so there should be H) and the net charge of this
residue is +0.117, which is physical nonsense. Based on the names and
suspect charges, it looks like you're just porting over a PRODRG
united-atom topology and trying to call it OPLS-AA. That's not going to
work.
Note that you also need [bonds] if you want the residue to actually be
chemically reasonable, otherwise it's just a collection of atoms sitting
near one another, which will immediately explode if you try to run a
simulation.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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