On 4/4/14, 8:47 AM, Ahmet yıldırım wrote:
Hi,
The bond types are set properly in ffbonded.itp. But I get the following
errors after grompp command. How can I fix it?
ERROR 1 [file protein_Ion_chain_A2.itp, line 33]:
No default Bond types
ERROR 2 [file protein_Ion_chain_A2.itp, line 34]:
No default Bond types
protein_Ion_chain_A2.itp:
[ moleculetype ]
; Name nrexcl
Ion_chain_A2 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 262 ZN rtp ZN q +2.0
1 Zn 262 ZN ZN 1 2 65.4 ;
qtot 2
If I'm remembering your model right, the Zn-HOH complex doesn't bear a +2 charge
on Zn. Is this what you actually want?
; residue 1001 OWZ rtp OWZ q +0.1
2 OZ 1001 OWZ OZ 2 -0.8824 16 ;
qtot 1.118
3 HZ 1001 OWZ HZ1 2 0.5001 1.008 ;
qtot 1.618
4 HZ 1001 OWZ HZ2 2 0.5001 1.008 ;
qtot 2.118
[ bonds ]
; ai aj funct c0 c1 c2 c3
2 3 1
2 4 1
Apparently whatever ffbonded.itp file that is being read doesn't have these
parameters. Unfortunately, there's not enough information to say why. If OZ-HZ
parameters were there, there would be no reason they wouldn't be read.
-Justin
[ angles ]
; ai aj ak funct c0 c1
c2 c3
3 2 4 1
; Include Position restraint file
#ifdef POSRES
#include "posre_Ion_chain_A2.itp"
#endif
2014-04-04 0:32 GMT+03:00 Justin Lemkul <jalem...@vt.edu>:
On 4/3/14, 2:58 PM, Gmail2 wrote:
Dear Justin,
Zn bound to three Histidine atoms and a water in carbonic anhydrase. This
water bound to Zn has different parameters than solvent water. That
parameters is present in literature. How should I set up such a system?
PS: I will use 'pdb2gmx' with -vsite hydrogens.
If you need virtual sites, then you need to figure out how to properly
build a virtual site database entry for that particular type of molecule.
That's entirely separate from any of the force field parameters you've
shown before, but realize that doing so negates most of the Zn-HOH bonded
parameters you posted.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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 601
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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