Esteban Gabriel Vega Hissi wrote:
Hi Justin,
You're right. The parameters in ffG53a6 are different from dmso.itp
file. I'll compare the results with the new simulations.
By the way, do you know if ffG53a6 DMSO parameters are updated to those
described in the paper you mention?
Not in any pre-built .itp file that I know of, but the .rtp entry for DMSO in
ffG53a6.rtp appears to have the correct charges. I assume, if you check the
atom types, that these are correct, as well.
-Justin
Thanks
Esteban
--
2010/4/30 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
Esteban Gabriel Vega Hissi wrote:
Hi,
I did the same and the simulations work properly! I think it's a
matter of labels.
Not entirely. It is a matter of force fields, which sometimes have
different atom nomenclature. The dmso.itp file assumes one is using
ffgmx. If using Gromos96, the atom types, and perhaps even some of
the parameters might have to be changed. There is a paper published
about a very good DMSO model using Gromos96; I would suggest
checking the parameters therein to be sure you're actually using a
valid model, and not some Frankenforcefield :)
-Justin
Esteban
UNSL
Argentina
--
2010/4/30 Saikat Banerjee <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
Hi,
I presume that there is a bug in gromacs-4.0.5.
When tried to run simulations with DMSO molecules there was
an error
report, which said:
"Fatal error:
Atomtype SD not found"
I checked extensively for the problem, and found that there is a
small error in the dmso.itp file present in
$GROMACS_INSTALL_DIR/share/gromacs/top/
Line 5 - 10 in dmso.itp file reads,
[ atoms ]
; nr type resnr residu atom cgnr charge
1 SD 1 DMSO SD 1 0.139
2 CD 1 DMSO CD1 1 0.16
3 OD 1 DMSO OD 1 -0.459
4 CD 1 DMSO CD2 1 0.16
I needed to change that to -
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 SDmso 1 DMSO SD 1 0.139 32.06000
2 CDmso 1 DMSO CD1 1 0.16 15.03500
3 ODmso 1 DMSO OD 1 -0.459 15.99940
4 CDmso 1 DMSO CD2 1 0.16 15.03500
Please note that the name of the type needed to be changed.
I am not sure if I was doing something wrong, or something was
erroneous in GROMACS. However, the above changes makes it work.
I just thought I would report this issue so that users know where
the problem is. I would like to request the GROMACS team to take
note of it and do the needful.
Thanks,
Saikat B.
--
-------------------------------------------------------------------
Saikat Banerjee
Integrated Ph.D student
Prof B. Bagchi's group
Room no. 210
Solid State and Structural Chemistry Unit (SSCU)
Indian Institute of Science
Bangalore-560012
Ph: +91-80-22933305 (lab)
+91-80-23602338 (lab)
+91-9980228606 (mobile)
Alternate e-mail:
[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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